Does this help Spencer? The read.delim() function assumes a tab character by
default, but I specifically included it using the read.csv function. The
downloaded file is NOT an Excel file so this should help.
GBM_protein_expression <- read.csv("C:/Users/Spencer/Desktop/GBM
protein_expression.tsv", sep=?\t?)
Sent from my iPhone
> On Dec 26, 2018, at 9:23 PM, Richard M. Heiberger <rmh at temple.edu>
wrote:
>
> this is wrong because the file is a csv file. read_excel is designed
> for xls files.
> GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM
> protein_expression.csv")
>
> How did you get a csv? it downloads as tsv.
>
> the statement you should use is in base, no library() statement is needed.
>
> GBM_protein_expression <- read.delim("C:/Users/Spencer/Desktop/GBM
> protein_expression.csv")
>
> read.delim is the same as read.csv except that it sets the sep
> argument to "\t".
>
>
>
> On Wed, Dec 26, 2018 at 11:11 PM Spencer Brackett
> <spbrackett20 at saintjosephhs.com> wrote:
>>
>> Sorry, my mistake.
>>
>> So I could still use read.table and should I try using a .txt version
of
>> the file to avoid the silent changes you described?
>>
>> Also, when I tried to simply this process by downloading the dataset
onto
>> RStudio opposed to R (Gui) I received the following...
>> library(readxl)
>>> GBM_protein_expression <-
read_excel("C:/Users/Spencer/Desktop/GBM
>> protein_expression.csv")
>> Error: Can't establish that the input is either xls or xlsx.
>>> View(GBM_protein_expression)
>> Error in View : object 'GBM_protein_expression' not found
>> Error in gzfile(file, mode) : cannot open the connection
>> In addition: Warning message:
>> In gzfile(file, mode) :
>> cannot open compressed file
>>
'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds',
>> probable reason 'No such file or directory'
>>> library(readxl)
>>> GBM_protein_expression <-
>> read_excel("C:/Users/Spencer/Desktop/GBM_protein_
expression.xlsx")
>> readxl works best with a newer version of the tibble package.
>> You currently have tibble v1.4.2.
>> Falling back to column name repair from tibble <= v1.4.2.
>> Message displays once per session.
>>> View(GBM_protein_expression)
>>
>>
>> Is this perhaps the result of lack of preview (which I did not complete
at
>> the time I hit import as the preview failed to load), or the fact that
the
>> excel file itself contains no numerical data, but only TRUE or FALSE
>> entries?
>>
>> On Wed, Dec 26, 2018 at 10:59 PM Jeff Newmiller <jdnewmil at
dcn.davis.ca.us>
>> wrote:
>>
>>> Please always reply-all to keep the list involved.
>>>
>>> If you used Save As to change the data format to Excel AND the file
>>> extension to xlsx, then yes, you should be able to read with
readxl. I
>>> don't recommend it, though... Excel often changes data silently
and in
>>> irregularly located places in your file.
>>>
>>> On December 26, 2018 7:38:16 PM PST, Spencer Brackett <
>>> spbrackett20 at saintjosephhs.com> wrote:
>>>> So even if I imported the file form ICGC to my desktop as an
excel
>>>> file,
>>>> and can view and saved the data as such, it is still a TSV?
>>>>
>>>> On Wed, Dec 26, 2018 at 10:35 PM Jeff Newmiller
>>>> <jdnewmil at dcn.davis.ca.us>
>>>> wrote:
>>>>
>>>>> CSV and TSV are not Excel files. Yes, I know Excel will
open them,
>>>> but
>>>>> that does not make them Excel files.
>>>>>
>>>>> Read a TSV file with read.table or read.csv, setting the
sep argument
>>>> to
>>>>> "\t".
>>>>>
>>>>> On December 26, 2018 7:26:35 PM PST, Spencer Brackett <
>>>>> spbrackett20 at saintjosephhs.com> wrote:
>>>>>> I tried importing the file without preview and recieved
the
>>>>>> following....
>>>>>>
>>>>>> library(readxl)
>>>>>>> GBM_protein_expression <-
read_excel("C:/Users/Spencer/Desktop/GBM
>>>>>> protein_expression.csv")
>>>>>> Error: Can't establish that the input is either xls
or xlsx.
>>>>>>> View(GBM_protein_expression)
>>>>>> Error in View : object 'GBM_protein_expression'
not found
>>>>>> Error in gzfile(file, mode) : cannot open the
connection
>>>>>> In addition: Warning message:
>>>>>> In gzfile(file, mode) :
>>>>>> cannot open compressed file
>>>>>
>>>>>
'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds',
>>>>>> probable reason 'No such file or directory'
>>>>>>> library(readxl)
>>>>>>> GBM_protein_expression <-
>>>>>> read_excel("C:/Users/Spencer/Desktop/GBM_protein_
expression.xlsx")
>>>>>> readxl works best with a newer version of the tibble
package.
>>>>>> You currently have tibble v1.4.2.
>>>>>> Falling back to column name repair from tibble <=
v1.4.2.
>>>>>> Message displays once per session.
>>>>>>> View(GBM_protein_expression)
>>>>>>
>>>>>> Also, the area above my console says that no data is
available in
>>>> the
>>>>>> table. Is this perhaps the result of lack of preview or
the fact
>>>> that
>>>>>> the
>>>>>> excel file itself contains no numerical data, but only
TRUE or FALSE
>>>>>> entries?
>>>>>>
>>>>>> On Wed, Dec 26, 2018 at 9:57 PM Spencer Brackett <
>>>>>> spbrackett20 at saintjosephhs.com> wrote:
>>>>>>
>>>>>>> Hello again,
>>>>>>>
>>>>>>> I worked on directly downloading the file into R as
was suggested,
>>>>>> but
>>>>>>> have thus far been unsuccessful. This is what I
generated on my
>>>>>> second
>>>>>>> attempt...
>>>>>>>
>>>>>>> GBM protein_expression<-(file.choose(),
header=TRUE, sep="\t")
>>>>>>> Error: unexpected symbol in "GBM
protein_expression"
>>>>>>>> GBM
>>>>>>>
>>>>>
>>>
>>>>>
protein_expression<-(file.choose(GBM_protein_expression.xlsx),header=TRUE,
>>>>>>> sep="\t")
>>>>>>> Error: unexpected symbol in "GBM
protein_expression"
>>>>>>>>
>>>>>>>
>>>>>>> What part of the argument is in error?
>>>>>>>
>>>>>>> Also I tried importing the dataset as an excel file
on RStudio to
>>>> see
>>>>>> if I
>>>>>>> could solve my problem that way. However, my
imported excel file
>>>> has
>>>>>> been
>>>>>>> stuck in the 'retrieving preview data' and
no data is appearing.
>>>> Is
>>>>>> the
>>>>>>> data file prehaps too large or in the wrong format?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Dec 26, 2018 at 6:42 PM Spencer Brackett
<
>>>>>>> spbrackett20 at saintjosephhs.com> wrote:
>>>>>>>
>>>>>>>> Mr. Heiberger,
>>>>>>>>
>>>>>>>> Thank you for the insight! I will try out
suggestion.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> Spencer Brackett
>>>>>>>>
>>>>>>>> On Wed, Dec 26, 2018 at 6:34 PM Richard M.
Heiberger
>>>>>> <rmh at temple.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I looked at the first file. It gives an
option to download as
>>>> TSV
>>>>>>>>> (tab separated values).
>>>>>>>>> That is the same as CSV except with tabs
instead of commas.
>>>>>>>>> You do not need any external software to
read it. Read the
>>>>>> downloaded
>>>>>>>>> file directly into R.
>>>>>>>>>
>>>>>>>>> read.delim looks as if it would work
directly on the downloaded
>>>>>> file.
>>>>>>>>> ?read.delim
>>>>>>>>> The notation "\t" means the tab
character.
>>>>>>>>>
>>>>>>>>> As an aside, stay away from notepad. it is
too naive for almost
>>>>>>>>> anything interesting.
>>>>>>>>> The specific case I often see is people
reading linux-style text
>>>>>> files
>>>>>>>>> with notepad, which doesn't
>>>>>>>>> understand NL terminated lines. nicely
formatted text files
>>>> become
>>>>>>>>> illegible.
>>>>>>>>>
>>>>>>>>> On Wed, Dec 26, 2018 at 6:04 PM Spencer
Brackett
>>>>>>>>> <spbrackett20 at saintjosephhs.com>
wrote:
>>>>>>>>>>
>>>>>>>>>> Good evening,
>>>>>>>>>>
>>>>>>>>>> I am attempting to anaylze the protein
expression data
>>>> contained
>>>>>> within
>>>>>>>>>> these two ICGC, TCGA datasets (one for
GBM and the other for
>>>> LGG)
>>>>>>>>>>
>>>>>>>>>> *File for GBM protein expression*:
>>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D
>>>>>>>>>>
>>>>>>>>>> *File for LGG protein expression:*
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> *
>>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22LGG-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D
>>>>>>>>>> <
>>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22LGG-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D
>>>>>>>>>> *
>>>>>>>>>>
>>>>>>>>>> When I tried to transfer the files
from .txt (via Notepad)
>>>> to
>>>>>> .csv
>>>>>>>>> (via
>>>>>>>>>> Excel), the data appeared in the
columns as unorganized and
>>>>>> random
>>>>>>>>>> script... not like how a typical csv
should be arranged at
>>>> all. I
>>>>>> need
>>>>>>>>> the
>>>>>>>>>> dataset to be converted into .csv in
order to analyze it in R,
>>>>>> which
>>>>>>>>> is why
>>>>>>>>>> I am hoping someone here might help me
in doing that. If not,
>>>> is
>>>>>> there
>>>>>>>>>> perhaps some other way that I could
analyze the datatsets on
>>>> R,
>>>>>> which
>>>>>>>>> again
>>>>>>>>>> is downloaded from the dataportal ICGC?
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>> Spencer Brackett
>>>>>>>>>>
>>>>>>>>>> [[alternative HTML version
deleted]]
>>>>>>>>>>
>>>>>>>>>>
______________________________________________
>>>>>>>>>> R-help at r-project.org mailing list --
To UNSUBSCRIBE and more,
>>>> see
>>>>>>>>>>
https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>>>>> PLEASE do read the posting guide
>>>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>>>>> and provide commented, minimal,
self-contained, reproducible
>>>>>> code.
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE
and more, see
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained,
reproducible code.
>>>>>
>>>>> --
>>>>> Sent from my phone. Please excuse my brevity.
>>>>>
>>>
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Caitlin, I tried your command in both RGui and RStudio but both came up as errors. I believe I made a mistake somewhere I labeling/downloading the files, which is the source of the confusion in R. I will re-examine the files saved on my desktop to determine the error. Regardless, would it be better to use a read.table or read.csv function when attempting to download my datasets? I tried using read.xl on RStudio as this process seemed much easier, however, it would seem that my proclivity to error prevents such. Best, Spencer On Wed, Dec 26, 2018 at 11:55 PM Caitlin Gibbons <bioprogrammer at gmail.com> wrote:> Does this help Spencer? The read.delim() function assumes a tab character > by default, but I specifically included it using the read.csv function. The > downloaded file is NOT an Excel file so this should help. > > GBM_protein_expression <- read.csv("C:/Users/Spencer/Desktop/GBM > protein_expression.tsv", sep=?\t?) > > Sent from my iPhone > > > On Dec 26, 2018, at 9:23 PM, Richard M. Heiberger <rmh at temple.edu> > wrote: > > > > this is wrong because the file is a csv file. read_excel is designed > > for xls files. > > GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM > > protein_expression.csv") > > > > How did you get a csv? it downloads as tsv. > > > > the statement you should use is in base, no library() statement is > needed. > > > > GBM_protein_expression <- read.delim("C:/Users/Spencer/Desktop/GBM > > protein_expression.csv") > > > > read.delim is the same as read.csv except that it sets the sep > > argument to "\t". > > > > > > > > On Wed, Dec 26, 2018 at 11:11 PM Spencer Brackett > > <spbrackett20 at saintjosephhs.com> wrote: > >> > >> Sorry, my mistake. > >> > >> So I could still use read.table and should I try using a .txt version of > >> the file to avoid the silent changes you described? > >> > >> Also, when I tried to simply this process by downloading the dataset > onto > >> RStudio opposed to R (Gui) I received the following... > >> library(readxl) > >>> GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM > >> protein_expression.csv") > >> Error: Can't establish that the input is either xls or xlsx. > >>> View(GBM_protein_expression) > >> Error in View : object 'GBM_protein_expression' not found > >> Error in gzfile(file, mode) : cannot open the connection > >> In addition: Warning message: > >> In gzfile(file, mode) : > >> cannot open compressed file > >> 'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds', > >> probable reason 'No such file or directory' > >>> library(readxl) > >>> GBM_protein_expression <- > >> read_excel("C:/Users/Spencer/Desktop/GBM_protein_ expression.xlsx") > >> readxl works best with a newer version of the tibble package. > >> You currently have tibble v1.4.2. > >> Falling back to column name repair from tibble <= v1.4.2. > >> Message displays once per session. > >>> View(GBM_protein_expression) > >> > >> > >> Is this perhaps the result of lack of preview (which I did not complete > at > >> the time I hit import as the preview failed to load), or the fact that > the > >> excel file itself contains no numerical data, but only TRUE or FALSE > >> entries? > >> > >> On Wed, Dec 26, 2018 at 10:59 PM Jeff Newmiller < > jdnewmil at dcn.davis.ca.us> > >> wrote: > >> > >>> Please always reply-all to keep the list involved. > >>> > >>> If you used Save As to change the data format to Excel AND the file > >>> extension to xlsx, then yes, you should be able to read with readxl. I > >>> don't recommend it, though... Excel often changes data silently and in > >>> irregularly located places in your file. > >>> > >>> On December 26, 2018 7:38:16 PM PST, Spencer Brackett < > >>> spbrackett20 at saintjosephhs.com> wrote: > >>>> So even if I imported the file form ICGC to my desktop as an excel > >>>> file, > >>>> and can view and saved the data as such, it is still a TSV? > >>>> > >>>> On Wed, Dec 26, 2018 at 10:35 PM Jeff Newmiller > >>>> <jdnewmil at dcn.davis.ca.us> > >>>> wrote: > >>>> > >>>>> CSV and TSV are not Excel files. Yes, I know Excel will open them, > >>>> but > >>>>> that does not make them Excel files. > >>>>> > >>>>> Read a TSV file with read.table or read.csv, setting the sep argument > >>>> to > >>>>> "\t". > >>>>> > >>>>> On December 26, 2018 7:26:35 PM PST, Spencer Brackett < > >>>>> spbrackett20 at saintjosephhs.com> wrote: > >>>>>> I tried importing the file without preview and recieved the > >>>>>> following.... > >>>>>> > >>>>>> library(readxl) > >>>>>>> GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM > >>>>>> protein_expression.csv") > >>>>>> Error: Can't establish that the input is either xls or xlsx. > >>>>>>> View(GBM_protein_expression) > >>>>>> Error in View : object 'GBM_protein_expression' not found > >>>>>> Error in gzfile(file, mode) : cannot open the connection > >>>>>> In addition: Warning message: > >>>>>> In gzfile(file, mode) : > >>>>>> cannot open compressed file > >>>>> > >>>>> > 'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds', > >>>>>> probable reason 'No such file or directory' > >>>>>>> library(readxl) > >>>>>>> GBM_protein_expression <- > >>>>>> read_excel("C:/Users/Spencer/Desktop/GBM_protein_ expression.xlsx") > >>>>>> readxl works best with a newer version of the tibble package. > >>>>>> You currently have tibble v1.4.2. > >>>>>> Falling back to column name repair from tibble <= v1.4.2. > >>>>>> Message displays once per session. > >>>>>>> View(GBM_protein_expression) > >>>>>> > >>>>>> Also, the area above my console says that no data is available in > >>>> the > >>>>>> table. Is this perhaps the result of lack of preview or the fact > >>>> that > >>>>>> the > >>>>>> excel file itself contains no numerical data, but only TRUE or FALSE > >>>>>> entries? > >>>>>> > >>>>>> On Wed, Dec 26, 2018 at 9:57 PM Spencer Brackett < > >>>>>> spbrackett20 at saintjosephhs.com> wrote: > >>>>>> > >>>>>>> Hello again, > >>>>>>> > >>>>>>> I worked on directly downloading the file into R as was suggested, > >>>>>> but > >>>>>>> have thus far been unsuccessful. This is what I generated on my > >>>>>> second > >>>>>>> attempt... > >>>>>>> > >>>>>>> GBM protein_expression<-(file.choose(), header=TRUE, sep="\t") > >>>>>>> Error: unexpected symbol in "GBM protein_expression" > >>>>>>>> GBM > >>>>>>> > >>>>> > >>> > >>>>> > protein_expression<-(file.choose(GBM_protein_expression.xlsx),header=TRUE, > >>>>>>> sep="\t") > >>>>>>> Error: unexpected symbol in "GBM protein_expression" > >>>>>>>> > >>>>>>> > >>>>>>> What part of the argument is in error? > >>>>>>> > >>>>>>> Also I tried importing the dataset as an excel file on RStudio to > >>>> see > >>>>>> if I > >>>>>>> could solve my problem that way. However, my imported excel file > >>>> has > >>>>>> been > >>>>>>> stuck in the 'retrieving preview data' and no data is appearing. > >>>> Is > >>>>>> the > >>>>>>> data file prehaps too large or in the wrong format? > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> On Wed, Dec 26, 2018 at 6:42 PM Spencer Brackett < > >>>>>>> spbrackett20 at saintjosephhs.com> wrote: > >>>>>>> > >>>>>>>> Mr. Heiberger, > >>>>>>>> > >>>>>>>> Thank you for the insight! I will try out suggestion. > >>>>>>>> > >>>>>>>> Best, > >>>>>>>> > >>>>>>>> Spencer Brackett > >>>>>>>> > >>>>>>>> On Wed, Dec 26, 2018 at 6:34 PM Richard M. Heiberger > >>>>>> <rmh at temple.edu> > >>>>>>>> wrote: > >>>>>>>> > >>>>>>>>> I looked at the first file. It gives an option to download as > >>>> TSV > >>>>>>>>> (tab separated values). > >>>>>>>>> That is the same as CSV except with tabs instead of commas. > >>>>>>>>> You do not need any external software to read it. Read the > >>>>>> downloaded > >>>>>>>>> file directly into R. > >>>>>>>>> > >>>>>>>>> read.delim looks as if it would work directly on the downloaded > >>>>>> file. > >>>>>>>>> ?read.delim > >>>>>>>>> The notation "\t" means the tab character. > >>>>>>>>> > >>>>>>>>> As an aside, stay away from notepad. it is too naive for almost > >>>>>>>>> anything interesting. > >>>>>>>>> The specific case I often see is people reading linux-style text > >>>>>> files > >>>>>>>>> with notepad, which doesn't > >>>>>>>>> understand NL terminated lines. nicely formatted text files > >>>> become > >>>>>>>>> illegible. > >>>>>>>>> > >>>>>>>>> On Wed, Dec 26, 2018 at 6:04 PM Spencer Brackett > >>>>>>>>> <spbrackett20 at saintjosephhs.com> wrote: > >>>>>>>>>> > >>>>>>>>>> Good evening, > >>>>>>>>>> > >>>>>>>>>> I am attempting to anaylze the protein expression data > >>>> contained > >>>>>> within > >>>>>>>>>> these two ICGC, TCGA datasets (one for GBM and the other for > >>>> LGG) > >>>>>>>>>> > >>>>>>>>>> *File for GBM protein expression*: > >>>>>>>>>> > >>>>>>>>> > >>>>>> > >>>>> > >>>> > >>> > https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D > >>>>>>>>>> > >>>>>>>>>> *File for LGG protein expression:* > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> * > >>>>>>>>> > >>>>>> > >>>>> > >>>> > >>> > https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22LGG-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D > >>>>>>>>>> < > >>>>>>>>> > >>>>>> > >>>>> > >>>> > >>> > https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22LGG-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D > >>>>>>>>>> * > >>>>>>>>>> > >>>>>>>>>> When I tried to transfer the files from .txt (via Notepad) > >>>> to > >>>>>> .csv > >>>>>>>>> (via > >>>>>>>>>> Excel), the data appeared in the columns as unorganized and > >>>>>> random > >>>>>>>>>> script... not like how a typical csv should be arranged at > >>>> all. I > >>>>>> need > >>>>>>>>> the > >>>>>>>>>> dataset to be converted into .csv in order to analyze it in R, > >>>>>> which > >>>>>>>>> is why > >>>>>>>>>> I am hoping someone here might help me in doing that. If not, > >>>> is > >>>>>> there > >>>>>>>>>> perhaps some other way that I could analyze the datatsets on > >>>> R, > >>>>>> which > >>>>>>>>> again > >>>>>>>>>> is downloaded from the dataportal ICGC? > >>>>>>>>>> > >>>>>>>>>> Best, > >>>>>>>>>> > >>>>>>>>>> Spencer Brackett > >>>>>>>>>> > >>>>>>>>>> [[alternative HTML version deleted]] > >>>>>>>>>> > >>>>>>>>>> ______________________________________________ > >>>>>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, > >>>> see > >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help > >>>>>>>>>> PLEASE do read the posting guide > >>>>>>>>> http://www.R-project.org/posting-guide.html > >>>>>>>>>> and provide commented, minimal, self-contained, reproducible > >>>>>> code. > >>>>>>>>> > >>>>>>>> > >>>>>> > >>>>>> [[alternative HTML version deleted]] > >>>>>> > >>>>>> ______________________________________________ > >>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-help > >>>>>> PLEASE do read the posting guide > >>>>>> http://www.R-project.org/posting-guide.html > >>>>>> and provide commented, minimal, self-contained, reproducible code. > >>>>> > >>>>> -- > >>>>> Sent from my phone. Please excuse my brevity. > >>>>> > >>> > >>> -- > >>> Sent from my phone. Please excuse my brevity. > >>> > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Follow up, Would read.txt also work, as I am certain that I have both datasets in .txt files? As to a previous users question concern the .csv nature of the supposed excel file, I am uncertain as to how this was translated as such. The file is most certainly in excel. On Thu, Dec 27, 2018 at 12:10 AM Spencer Brackett < spbrackett20 at saintjosephhs.com> wrote:> Caitlin, > > I tried your command in both RGui and RStudio but both came up as > errors. I believe I made a mistake somewhere I labeling/downloading the > files, which is the source of the confusion in R. I will re-examine the > files saved on my desktop to determine the error. Regardless, would it be > better to use a read.table or read.csv function when attempting to download > my datasets? I tried using read.xl on RStudio as this process seemed much > easier, however, it would seem that my proclivity to error prevents such. > > Best, > > Spencer > > On Wed, Dec 26, 2018 at 11:55 PM Caitlin Gibbons <bioprogrammer at gmail.com> > wrote: > >> Does this help Spencer? The read.delim() function assumes a tab character >> by default, but I specifically included it using the read.csv function. The >> downloaded file is NOT an Excel file so this should help. >> >> GBM_protein_expression <- read.csv("C:/Users/Spencer/Desktop/GBM >> protein_expression.tsv", sep=?\t?) >> >> Sent from my iPhone >> >> > On Dec 26, 2018, at 9:23 PM, Richard M. Heiberger <rmh at temple.edu> >> wrote: >> > >> > this is wrong because the file is a csv file. read_excel is designed >> > for xls files. >> > GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM >> > protein_expression.csv") >> > >> > How did you get a csv? it downloads as tsv. >> > >> > the statement you should use is in base, no library() statement is >> needed. >> > >> > GBM_protein_expression <- read.delim("C:/Users/Spencer/Desktop/GBM >> > protein_expression.csv") >> > >> > read.delim is the same as read.csv except that it sets the sep >> > argument to "\t". >> > >> > >> > >> > On Wed, Dec 26, 2018 at 11:11 PM Spencer Brackett >> > <spbrackett20 at saintjosephhs.com> wrote: >> >> >> >> Sorry, my mistake. >> >> >> >> So I could still use read.table and should I try using a .txt version >> of >> >> the file to avoid the silent changes you described? >> >> >> >> Also, when I tried to simply this process by downloading the dataset >> onto >> >> RStudio opposed to R (Gui) I received the following... >> >> library(readxl) >> >>> GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM >> >> protein_expression.csv") >> >> Error: Can't establish that the input is either xls or xlsx. >> >>> View(GBM_protein_expression) >> >> Error in View : object 'GBM_protein_expression' not found >> >> Error in gzfile(file, mode) : cannot open the connection >> >> In addition: Warning message: >> >> In gzfile(file, mode) : >> >> cannot open compressed file >> >> 'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds', >> >> probable reason 'No such file or directory' >> >>> library(readxl) >> >>> GBM_protein_expression <- >> >> read_excel("C:/Users/Spencer/Desktop/GBM_protein_ expression.xlsx") >> >> readxl works best with a newer version of the tibble package. >> >> You currently have tibble v1.4.2. >> >> Falling back to column name repair from tibble <= v1.4.2. >> >> Message displays once per session. >> >>> View(GBM_protein_expression) >> >> >> >> >> >> Is this perhaps the result of lack of preview (which I did not >> complete at >> >> the time I hit import as the preview failed to load), or the fact that >> the >> >> excel file itself contains no numerical data, but only TRUE or FALSE >> >> entries? >> >> >> >> On Wed, Dec 26, 2018 at 10:59 PM Jeff Newmiller < >> jdnewmil at dcn.davis.ca.us> >> >> wrote: >> >> >> >>> Please always reply-all to keep the list involved. >> >>> >> >>> If you used Save As to change the data format to Excel AND the file >> >>> extension to xlsx, then yes, you should be able to read with readxl. I >> >>> don't recommend it, though... Excel often changes data silently and in >> >>> irregularly located places in your file. >> >>> >> >>> On December 26, 2018 7:38:16 PM PST, Spencer Brackett < >> >>> spbrackett20 at saintjosephhs.com> wrote: >> >>>> So even if I imported the file form ICGC to my desktop as an excel >> >>>> file, >> >>>> and can view and saved the data as such, it is still a TSV? >> >>>> >> >>>> On Wed, Dec 26, 2018 at 10:35 PM Jeff Newmiller >> >>>> <jdnewmil at dcn.davis.ca.us> >> >>>> wrote: >> >>>> >> >>>>> CSV and TSV are not Excel files. Yes, I know Excel will open them, >> >>>> but >> >>>>> that does not make them Excel files. >> >>>>> >> >>>>> Read a TSV file with read.table or read.csv, setting the sep >> argument >> >>>> to >> >>>>> "\t". >> >>>>> >> >>>>> On December 26, 2018 7:26:35 PM PST, Spencer Brackett < >> >>>>> spbrackett20 at saintjosephhs.com> wrote: >> >>>>>> I tried importing the file without preview and recieved the >> >>>>>> following.... >> >>>>>> >> >>>>>> library(readxl) >> >>>>>>> GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM >> >>>>>> protein_expression.csv") >> >>>>>> Error: Can't establish that the input is either xls or xlsx. >> >>>>>>> View(GBM_protein_expression) >> >>>>>> Error in View : object 'GBM_protein_expression' not found >> >>>>>> Error in gzfile(file, mode) : cannot open the connection >> >>>>>> In addition: Warning message: >> >>>>>> In gzfile(file, mode) : >> >>>>>> cannot open compressed file >> >>>>> >> >>>>> >> 'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds', >> >>>>>> probable reason 'No such file or directory' >> >>>>>>> library(readxl) >> >>>>>>> GBM_protein_expression <- >> >>>>>> read_excel("C:/Users/Spencer/Desktop/GBM_protein_ expression.xlsx") >> >>>>>> readxl works best with a newer version of the tibble package. >> >>>>>> You currently have tibble v1.4.2. >> >>>>>> Falling back to column name repair from tibble <= v1.4.2. >> >>>>>> Message displays once per session. >> >>>>>>> View(GBM_protein_expression) >> >>>>>> >> >>>>>> Also, the area above my console says that no data is available in >> >>>> the >> >>>>>> table. Is this perhaps the result of lack of preview or the fact >> >>>> that >> >>>>>> the >> >>>>>> excel file itself contains no numerical data, but only TRUE or >> FALSE >> >>>>>> entries? >> >>>>>> >> >>>>>> On Wed, Dec 26, 2018 at 9:57 PM Spencer Brackett < >> >>>>>> spbrackett20 at saintjosephhs.com> wrote: >> >>>>>> >> >>>>>>> Hello again, >> >>>>>>> >> >>>>>>> I worked on directly downloading the file into R as was suggested, >> >>>>>> but >> >>>>>>> have thus far been unsuccessful. This is what I generated on my >> >>>>>> second >> >>>>>>> attempt... >> >>>>>>> >> >>>>>>> GBM protein_expression<-(file.choose(), header=TRUE, sep="\t") >> >>>>>>> Error: unexpected symbol in "GBM protein_expression" >> >>>>>>>> GBM >> >>>>>>> >> >>>>> >> >>> >> >>>>> >> protein_expression<-(file.choose(GBM_protein_expression.xlsx),header=TRUE, >> >>>>>>> sep="\t") >> >>>>>>> Error: unexpected symbol in "GBM protein_expression" >> >>>>>>>> >> >>>>>>> >> >>>>>>> What part of the argument is in error? >> >>>>>>> >> >>>>>>> Also I tried importing the dataset as an excel file on RStudio to >> >>>> see >> >>>>>> if I >> >>>>>>> could solve my problem that way. However, my imported excel file >> >>>> has >> >>>>>> been >> >>>>>>> stuck in the 'retrieving preview data' and no data is appearing. >> >>>> Is >> >>>>>> the >> >>>>>>> data file prehaps too large or in the wrong format? >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> On Wed, Dec 26, 2018 at 6:42 PM Spencer Brackett < >> >>>>>>> spbrackett20 at saintjosephhs.com> wrote: >> >>>>>>> >> >>>>>>>> Mr. Heiberger, >> >>>>>>>> >> >>>>>>>> Thank you for the insight! I will try out suggestion. >> >>>>>>>> >> >>>>>>>> Best, >> >>>>>>>> >> >>>>>>>> Spencer Brackett >> >>>>>>>> >> >>>>>>>> On Wed, Dec 26, 2018 at 6:34 PM Richard M. Heiberger >> >>>>>> <rmh at temple.edu> >> >>>>>>>> wrote: >> >>>>>>>> >> >>>>>>>>> I looked at the first file. It gives an option to download as >> >>>> TSV >> >>>>>>>>> (tab separated values). >> >>>>>>>>> That is the same as CSV except with tabs instead of commas. >> >>>>>>>>> You do not need any external software to read it. Read the >> >>>>>> downloaded >> >>>>>>>>> file directly into R. >> >>>>>>>>> >> >>>>>>>>> read.delim looks as if it would work directly on the downloaded >> >>>>>> file. >> >>>>>>>>> ?read.delim >> >>>>>>>>> The notation "\t" means the tab character. >> >>>>>>>>> >> >>>>>>>>> As an aside, stay away from notepad. it is too naive for almost >> >>>>>>>>> anything interesting. >> >>>>>>>>> The specific case I often see is people reading linux-style text >> >>>>>> files >> >>>>>>>>> with notepad, which doesn't >> >>>>>>>>> understand NL terminated lines. nicely formatted text files >> >>>> become >> >>>>>>>>> illegible. >> >>>>>>>>> >> >>>>>>>>> On Wed, Dec 26, 2018 at 6:04 PM Spencer Brackett >> >>>>>>>>> <spbrackett20 at saintjosephhs.com> wrote: >> >>>>>>>>>> >> >>>>>>>>>> Good evening, >> >>>>>>>>>> >> >>>>>>>>>> I am attempting to anaylze the protein expression data >> >>>> contained >> >>>>>> within >> >>>>>>>>>> these two ICGC, TCGA datasets (one for GBM and the other for >> >>>> LGG) >> >>>>>>>>>> >> >>>>>>>>>> *File for GBM protein expression*: >> >>>>>>>>>> >> >>>>>>>>> >> >>>>>> >> >>>>> >> >>>> >> >>> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D >> >>>>>>>>>> >> >>>>>>>>>> *File for LGG protein expression:* >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> * >> >>>>>>>>> >> >>>>>> >> >>>>> >> >>>> >> >>> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22LGG-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D >> >>>>>>>>>> < >> >>>>>>>>> >> >>>>>> >> >>>>> >> >>>> >> >>> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22LGG-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D >> >>>>>>>>>> * >> >>>>>>>>>> >> >>>>>>>>>> When I tried to transfer the files from .txt (via Notepad) >> >>>> to >> >>>>>> .csv >> >>>>>>>>> (via >> >>>>>>>>>> Excel), the data appeared in the columns as unorganized and >> >>>>>> random >> >>>>>>>>>> script... not like how a typical csv should be arranged at >> >>>> all. I >> >>>>>> need >> >>>>>>>>> the >> >>>>>>>>>> dataset to be converted into .csv in order to analyze it in R, >> >>>>>> which >> >>>>>>>>> is why >> >>>>>>>>>> I am hoping someone here might help me in doing that. If not, >> >>>> is >> >>>>>> there >> >>>>>>>>>> perhaps some other way that I could analyze the datatsets on >> >>>> R, >> >>>>>> which >> >>>>>>>>> again >> >>>>>>>>>> is downloaded from the dataportal ICGC? >> >>>>>>>>>> >> >>>>>>>>>> Best, >> >>>>>>>>>> >> >>>>>>>>>> Spencer Brackett >> >>>>>>>>>> >> >>>>>>>>>> [[alternative HTML version deleted]] >> >>>>>>>>>> >> >>>>>>>>>> ______________________________________________ >> >>>>>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, >> >>>> see >> >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help >> >>>>>>>>>> PLEASE do read the posting guide >> >>>>>>>>> http://www.R-project.org/posting-guide.html >> >>>>>>>>>> and provide commented, minimal, self-contained, reproducible >> >>>>>> code. >> >>>>>>>>> >> >>>>>>>> >> >>>>>> >> >>>>>> [[alternative HTML version deleted]] >> >>>>>> >> >>>>>> ______________________________________________ >> >>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-help >> >>>>>> PLEASE do read the posting guide >> >>>>>> http://www.R-project.org/posting-guide.html >> >>>>>> and provide commented, minimal, self-contained, reproducible code. >> >>>>> >> >>>>> -- >> >>>>> Sent from my phone. Please excuse my brevity. >> >>>>> >> >>> >> >>> -- >> >>> Sent from my phone. Please excuse my brevity. >> >>> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> ______________________________________________ >> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> >> https://stat.ethz.ch/mailman/listinfo/r-help >> >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> >> and provide commented, minimal, self-contained, reproducible code. >> > >> > ______________________________________________ >> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> > https://stat.ethz.ch/mailman/listinfo/r-help >> > PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> > and provide commented, minimal, self-contained, reproducible code. >> >[[alternative HTML version deleted]]