My apologies... the following is what I received from the correction the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",") Warning messages: 1: In read.table(file = file, header = header, sep = sep, quote = quote, : line 3 appears to contain embedded nulls 2: In read.table(file = file, header = header, sep = sep, quote = quote, : line 4 appears to contain embedded nulls 3: In read.table(file = file, header = header, sep = sep, quote = quote, : line 5 appears to contain embedded nulls 4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : embedded nul(s) found in input>On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdbarry at alaska.edu> wrote:> You still haven't fixed the first thing both Sarah and I pointed out. You > are lacking an = between sep and "," > > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") > > should be > > the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE, *sep > = ","*) > > as Sarah pointed out, you should use spaces to help make these errors more > obvious. > > On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett < > spbrackett20 at saintjosephhs.com> wrote: > >> Hello again, >> >> My apologies for the delayed response... computer troubles. In reference >> to >> Ms. Goslee's and Mr. Barry's query, the following is the error code >> received after I inputted my R command >> >> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >> Error: unexpected string constant in >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep","" >> >> Given this, should I proceed with implementing the path<getwd() ,since I >> am, as he suggested trying to set the variable *path* to my working >> directory with path<-"." >> >> Mr. Mittal also recommended importing with r studio, which I shall try in >> the meantime. >> >> Many thanks, >> >> Spencer Brackett >> >> >> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal <prof.amit.mittal at gmail.com> >> wrote: >> >> > Use r studio and import from the menu. Read_csv has changed >> > >> > Also you can see any format problems >> > >> > On Thu, 30 Aug 2018 3:36 am Spencer Brackett, < >> > spbrackett20 at saintjosephhs.com> wrote: >> > >> >> Good evening R users, >> >> >> >> I am attempting to carry out DNA methylation analysis on two separate >> >> CSV >> >> files (LGG and GBM), which I have downloaded onto my R console. To set >> the >> >> path<-"." to be indicative of one or both of the csv files, I utilized >> the >> >> following functions and received the errors shown. How do I set the >> "." so >> >> that I can begin analysis on my files? >> >> >> >> > the_data <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",") >> >> Error: unexpected string constant in "the_data >> >> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep","" >> >> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",") >> >> Error: unexpected string constant in >> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep","" >> >> >> >> This is the preliminary portion of the analysis I am trying to run, >> which >> >> I >> >> am referring to: >> >> >> >> 1 library(TCGAbiolinks) >> >> 2 >> >> 3 # Download the DNA methylation data: HumanMethylation450 LGG and GBM. >> >> 4 path <? "." >> >> 5 >> >> 6 query.met <? TCGAquery(tumor = c("LGG","GBM"),"HumanMethylation450", >> >> level = 3) >> >> 7 TCGAdownload(query.met, path = path ) >> >> 8 met <? TCGAprepare(query = query.met,dir = path, >> >> 9 add.subtype = TRUE, add.clinical = TRUE, >> >> 10 summarizedExperiment = TRUE, >> >> 11 save = TRUE, filename = "lgg_gbm_met.rda") >> >> 12 >> >> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and GBM. >> >> 14 query.exp <? TCGAquery(tumor = c("lgg","gbm"), platform >> >> "IlluminaHiSeq_ >> >> RNASeqV2",level = 3) >> >> 15 >> >> 16 TCGAdownload(query.exp,path = path, type = "rsem.genes.normalized_ >> >> results") >> >> 17 >> >> 18 exp <? TCGAprepare(query = query.exp, dir = path, >> >> 19 summarizedExperiment = TRUE, >> >> 20 add.subtype = TRUE, add.clinical = TRUE, >> >> 21 type = "rsem.genes.normalized_results", >> >> 22 save = T,filename = "lgg_gbm_exp.rda") >> >> >> >> Many thanks, >> >> >> >> 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. >> > >[[alternative HTML version deleted]]
At this point, it seems pretty clear that the issue is in the data file itself. Possibilities are that it is either not a CSV file to begin with or in some exotic encoding (utf-16?). You probably need to look at the file in a text editor to see whether the context makes sense as comma-separated variables. Also, perhaps review the download mechanism --- recently I have found several students shooting themselves in the foot by downloading .csv files, having them automatically opened by Excel and the save them _in_ Excel, garbling the file in the process. -pd> On 31 Aug 2018, at 03:05 , Spencer Brackett <spbrackett20 at saintjosephhs.com> wrote: > > My apologies... the following is what I received from the correction > > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",") > Warning messages: > 1: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 3 appears to contain embedded nulls > 2: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 4 appears to contain embedded nulls > 3: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 5 appears to contain embedded nulls > 4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : > embedded nul(s) found in input >> > > > On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdbarry at alaska.edu> wrote: > >> You still haven't fixed the first thing both Sarah and I pointed out. You >> are lacking an = between sep and "," >> >> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >> >> should be >> >> the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE, *sep >> = ","*) >> >> as Sarah pointed out, you should use spaces to help make these errors more >> obvious. >> >> On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett < >> spbrackett20 at saintjosephhs.com> wrote: >> >>> Hello again, >>> >>> My apologies for the delayed response... computer troubles. In reference >>> to >>> Ms. Goslee's and Mr. Barry's query, the following is the error code >>> received after I inputted my R command >>> >>> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >>> Error: unexpected string constant in >>> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep","" >>> >>> Given this, should I proceed with implementing the path<getwd() ,since I >>> am, as he suggested trying to set the variable *path* to my working >>> directory with path<-"." >>> >>> Mr. Mittal also recommended importing with r studio, which I shall try in >>> the meantime. >>> >>> Many thanks, >>> >>> Spencer Brackett >>> >>> >>> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal <prof.amit.mittal at gmail.com> >>> wrote: >>> >>>> Use r studio and import from the menu. Read_csv has changed >>>> >>>> Also you can see any format problems >>>> >>>> On Thu, 30 Aug 2018 3:36 am Spencer Brackett, < >>>> spbrackett20 at saintjosephhs.com> wrote: >>>> >>>>> Good evening R users, >>>>> >>>>> I am attempting to carry out DNA methylation analysis on two separate >>>>> CSV >>>>> files (LGG and GBM), which I have downloaded onto my R console. To set >>> the >>>>> path<-"." to be indicative of one or both of the csv files, I utilized >>> the >>>>> following functions and received the errors shown. How do I set the >>> "." so >>>>> that I can begin analysis on my files? >>>>> >>>>>> the_data <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",") >>>>> Error: unexpected string constant in "the_data >>>>> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep","" >>>>>> the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",") >>>>> Error: unexpected string constant in >>>>> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep","" >>>>> >>>>> This is the preliminary portion of the analysis I am trying to run, >>> which >>>>> I >>>>> am referring to: >>>>> >>>>> 1 library(TCGAbiolinks) >>>>> 2 >>>>> 3 # Download the DNA methylation data: HumanMethylation450 LGG and GBM. >>>>> 4 path <? "." >>>>> 5 >>>>> 6 query.met <? TCGAquery(tumor = c("LGG","GBM"),"HumanMethylation450", >>>>> level = 3) >>>>> 7 TCGAdownload(query.met, path = path ) >>>>> 8 met <? TCGAprepare(query = query.met,dir = path, >>>>> 9 add.subtype = TRUE, add.clinical = TRUE, >>>>> 10 summarizedExperiment = TRUE, >>>>> 11 save = TRUE, filename = "lgg_gbm_met.rda") >>>>> 12 >>>>> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and GBM. >>>>> 14 query.exp <? TCGAquery(tumor = c("lgg","gbm"), platform >>>>> "IlluminaHiSeq_ >>>>> RNASeqV2",level = 3) >>>>> 15 >>>>> 16 TCGAdownload(query.exp,path = path, type = "rsem.genes.normalized_ >>>>> results") >>>>> 17 >>>>> 18 exp <? TCGAprepare(query = query.exp, dir = path, >>>>> 19 summarizedExperiment = TRUE, >>>>> 20 add.subtype = TRUE, add.clinical = TRUE, >>>>> 21 type = "rsem.genes.normalized_results", >>>>> 22 save = T,filename = "lgg_gbm_exp.rda") >>>>> >>>>> Many thanks, >>>>> >>>>> 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. >>> >> >> > > [[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.-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
Try adding fileEncoding="UTF-16" to your read.csv() call. Many Windows programs write UTF-16 files by default. Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Aug 30, 2018 at 6:05 PM, Spencer Brackett < spbrackett20 at saintjosephhs.com> wrote:> My apologies... the following is what I received from the correction > > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",") > Warning messages: > 1: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 3 appears to contain embedded nulls > 2: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 4 appears to contain embedded nulls > 3: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 5 appears to contain embedded nulls > 4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, > : > embedded nul(s) found in input > > > > > On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdbarry at alaska.edu> wrote: > > > You still haven't fixed the first thing both Sarah and I pointed out. You > > are lacking an = between sep and "," > > > > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") > > > > should be > > > > the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE, *sep > > = ","*) > > > > as Sarah pointed out, you should use spaces to help make these errors > more > > obvious. > > > > On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett < > > spbrackett20 at saintjosephhs.com> wrote: > > > >> Hello again, > >> > >> My apologies for the delayed response... computer troubles. In reference > >> to > >> Ms. Goslee's and Mr. Barry's query, the following is the error code > >> received after I inputted my R command > >> > >> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") > >> Error: unexpected string constant in > >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep","" > >> > >> Given this, should I proceed with implementing the path<getwd() ,since I > >> am, as he suggested trying to set the variable *path* to my working > >> directory with path<-"." > >> > >> Mr. Mittal also recommended importing with r studio, which I shall try > in > >> the meantime. > >> > >> Many thanks, > >> > >> Spencer Brackett > >> > >> > >> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal < > prof.amit.mittal at gmail.com> > >> wrote: > >> > >> > Use r studio and import from the menu. Read_csv has changed > >> > > >> > Also you can see any format problems > >> > > >> > On Thu, 30 Aug 2018 3:36 am Spencer Brackett, < > >> > spbrackett20 at saintjosephhs.com> wrote: > >> > > >> >> Good evening R users, > >> >> > >> >> I am attempting to carry out DNA methylation analysis on two > separate > >> >> CSV > >> >> files (LGG and GBM), which I have downloaded onto my R console. To > set > >> the > >> >> path<-"." to be indicative of one or both of the csv files, I > utilized > >> the > >> >> following functions and received the errors shown. How do I set the > >> "." so > >> >> that I can begin analysis on my files? > >> >> > >> >> > the_data <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",") > >> >> Error: unexpected string constant in "the_data > >> >> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep","" > >> >> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",") > >> >> Error: unexpected string constant in > >> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep","" > >> >> > >> >> This is the preliminary portion of the analysis I am trying to run, > >> which > >> >> I > >> >> am referring to: > >> >> > >> >> 1 library(TCGAbiolinks) > >> >> 2 > >> >> 3 # Download the DNA methylation data: HumanMethylation450 LGG and > GBM. > >> >> 4 path <? "." > >> >> 5 > >> >> 6 query.met <? TCGAquery(tumor = c("LGG","GBM")," > HumanMethylation450", > >> >> level = 3) > >> >> 7 TCGAdownload(query.met, path = path ) > >> >> 8 met <? TCGAprepare(query = query.met,dir = path, > >> >> 9 add.subtype = TRUE, add.clinical = TRUE, > >> >> 10 summarizedExperiment = TRUE, > >> >> 11 save = TRUE, filename = "lgg_gbm_met.rda") > >> >> 12 > >> >> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and > GBM. > >> >> 14 query.exp <? TCGAquery(tumor = c("lgg","gbm"), platform > >> >> "IlluminaHiSeq_ > >> >> RNASeqV2",level = 3) > >> >> 15 > >> >> 16 TCGAdownload(query.exp,path = path, type = "rsem.genes.normalized_ > >> >> results") > >> >> 17 > >> >> 18 exp <? TCGAprepare(query = query.exp, dir = path, > >> >> 19 summarizedExperiment = TRUE, > >> >> 20 add.subtype = TRUE, add.clinical = TRUE, > >> >> 21 type = "rsem.genes.normalized_results", > >> >> 22 save = T,filename = "lgg_gbm_exp.rda") > >> >> > >> >> Many thanks, > >> >> > >> >> 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. > >> > > > > > > [[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]]
It looks like it is not a UTF-16 text file, although it could be UTF-16 with a different byte order. Look at it with a text editor or Excel or 'od' or 'file' (the latter are Unix utilities) or ask the person you got it from to see what the file contains. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Aug 31, 2018 at 6:01 PM, Spencer Brackett < spbrackett20 at saintjosephhs.com> wrote:> Thank you Mr. Dunlap for the suggestion. How would this modified read.csv > file read? This is my attempt at what you suggested, which is obviously > errored. > > > the_data<-read.csv(file="GBM_clinical_drug.csv",header> TRUE,fileEncoding="UTF-16") > Warning messages: > 1: In read.table(file = file, header = header, sep = sep, quote = quote, : > invalid input found on input connection 'GBM_clinical_drug.csv' > 2: In read.table(file = file, header = header, sep = sep, quote = quote, : > incomplete final line found by readTableHeader on 'GBM_clinical_drug.csv' > > the_data<-read.csv(file="GBM_clinical_drug.csv",header> TRUE,sep=",",fileEncoding="UTF-16") > Warning messages: > 1: In read.table(file = file, header = header, sep = sep, quote = quote, : > invalid input found on input connection 'GBM_clinical_drug.csv' > 2: In read.table(file = file, header = header, sep = sep, quote = quote, : > incomplete final line found by readTableHeader on 'GBM_clinical_drug.csv' > > Many thanks, > > Spencer Brackett > > > > > On Fri, Aug 31, 2018 at 11:12 AM William Dunlap <wdunlap at tibco.com> wrote: > >> Try adding fileEncoding="UTF-16" to your read.csv() call. Many Windows >> programs write UTF-16 files by default. >> >> Bill Dunlap >> TIBCO Software >> wdunlap tibco.com >> >> On Thu, Aug 30, 2018 at 6:05 PM, Spencer Brackett < >> spbrackett20 at saintjosephhs.com> wrote: >> >>> My apologies... the following is what I received from the correction >>> >>> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",") >>> Warning messages: >>> 1: In read.table(file = file, header = header, sep = sep, quote >>> quote, : >>> line 3 appears to contain embedded nulls >>> 2: In read.table(file = file, header = header, sep = sep, quote >>> quote, : >>> line 4 appears to contain embedded nulls >>> 3: In read.table(file = file, header = header, sep = sep, quote >>> quote, : >>> line 5 appears to contain embedded nulls >>> 4: In scan(file = file, what = what, sep = sep, quote = quote, dec >>> dec, : >>> embedded nul(s) found in input >>> > >>> >>> >>> On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdbarry at alaska.edu> >>> wrote: >>> >>> > You still haven't fixed the first thing both Sarah and I pointed out. >>> You >>> > are lacking an = between sep and "," >>> > >>> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >>> > >>> > should be >>> > >>> > the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE, >>> *sep >>> > = ","*) >>> > >>> > as Sarah pointed out, you should use spaces to help make these errors >>> more >>> > obvious. >>> > >>> > On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett < >>> > spbrackett20 at saintjosephhs.com> wrote: >>> > >>> >> Hello again, >>> >> >>> >> My apologies for the delayed response... computer troubles. In >>> reference >>> >> to >>> >> Ms. Goslee's and Mr. Barry's query, the following is the error code >>> >> received after I inputted my R command >>> >> >>> >> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >>> >> Error: unexpected string constant in >>> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep","" >>> >> >>> >> Given this, should I proceed with implementing the path<getwd() >>> ,since I >>> >> am, as he suggested trying to set the variable *path* to my working >>> >> directory with path<-"." >>> >> >>> >> Mr. Mittal also recommended importing with r studio, which I shall >>> try in >>> >> the meantime. >>> >> >>> >> Many thanks, >>> >> >>> >> Spencer Brackett >>> >> >>> >> >>> >> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal < >>> prof.amit.mittal at gmail.com> >>> >> wrote: >>> >> >>> >> > Use r studio and import from the menu. Read_csv has changed >>> >> > >>> >> > Also you can see any format problems >>> >> > >>> >> > On Thu, 30 Aug 2018 3:36 am Spencer Brackett, < >>> >> > spbrackett20 at saintjosephhs.com> wrote: >>> >> > >>> >> >> Good evening R users, >>> >> >> >>> >> >> I am attempting to carry out DNA methylation analysis on two >>> separate >>> >> >> CSV >>> >> >> files (LGG and GBM), which I have downloaded onto my R console. To >>> set >>> >> the >>> >> >> path<-"." to be indicative of one or both of the csv files, I >>> utilized >>> >> the >>> >> >> following functions and received the errors shown. How do I set the >>> >> "." so >>> >> >> that I can begin analysis on my files? >>> >> >> >>> >> >> > the_data <-read.csv(file="LGG_clinical_ >>> drug.csv",header=T,sep",") >>> >> >> Error: unexpected string constant in "the_data >>> >> >> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep","" >>> >> >> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",") >>> >> >> Error: unexpected string constant in >>> >> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep","" >>> >> >> >>> >> >> This is the preliminary portion of the analysis I am trying to run, >>> >> which >>> >> >> I >>> >> >> am referring to: >>> >> >> >>> >> >> 1 library(TCGAbiolinks) >>> >> >> 2 >>> >> >> 3 # Download the DNA methylation data: HumanMethylation450 LGG and >>> GBM. >>> >> >> 4 path <? "." >>> >> >> 5 >>> >> >> 6 query.met <? TCGAquery(tumor = c("LGG","GBM")," >>> HumanMethylation450", >>> >> >> level = 3) >>> >> >> 7 TCGAdownload(query.met, path = path ) >>> >> >> 8 met <? TCGAprepare(query = query.met,dir = path, >>> >> >> 9 add.subtype = TRUE, add.clinical = TRUE, >>> >> >> 10 summarizedExperiment = TRUE, >>> >> >> 11 save = TRUE, filename = "lgg_gbm_met.rda") >>> >> >> 12 >>> >> >> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and >>> GBM. >>> >> >> 14 query.exp <? TCGAquery(tumor = c("lgg","gbm"), platform >>> >> >> "IlluminaHiSeq_ >>> >> >> RNASeqV2",level = 3) >>> >> >> 15 >>> >> >> 16 TCGAdownload(query.exp,path = path, type >>> "rsem.genes.normalized_ >>> >> >> results") >>> >> >> 17 >>> >> >> 18 exp <? TCGAprepare(query = query.exp, dir = path, >>> >> >> 19 summarizedExperiment = TRUE, >>> >> >> 20 add.subtype = TRUE, add.clinical = TRUE, >>> >> >> 21 type = "rsem.genes.normalized_results", >>> >> >> 22 save = T,filename = "lgg_gbm_exp.rda") >>> >> >> >>> >> >> Many thanks, >>> >> >> >>> >> >> 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. >>> >> >>> > >>> > >>> >>> [[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]]