Displaying 5 results from an estimated 5 matches for "2ecel".
2018 May 02
7
download.file does not process gz files correctly (truncates them?)
....CEL.gz . If I download this
manually and try
oligo::read.celfiles("GSM907811.CEL.gz")
everything works fine. (oligo is a bioConductor package)
However, if I download using
download.file("
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz
",
destfile = "GSM907811.CEL.gz")
The file is downloaded, but oligo::read.celfiles() returns the following
error:
Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
End of gz file reached unexpectedly. Perhaps this file is truncated.
M...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...download.file() is actually larger (in this case by about 8 kb). The
file xxx_inR.CEL.gz is read in using:
setwd("E:/Temp/genexpr/Compare")
id <- "GSM907854"
flink <- paste0("
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907854&format=file&file=GSM907854%2ECEL%2Egz
")
fname <- paste0(id,"_inR.CEL.gz")
download.file(flink,
destfile = fname)
The file xxx_direct.CEL.gz is downloaded from
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907854 (download link
at the bottom of the page).
Output of dir in CMD:
05/03/2018...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...>
> oligo::read.celfiles("GSM907811.CEL.gz")
>
> everything works fine. (oligo is a bioConductor package)
>
> However, if I download using
>
> download.file("
> https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz
> ",
> destfile = "GSM907811.CEL.gz")
On windows, the 'mode' argument to download.file() needs to be "wb"
(write binary) for binary files.
Martin
>
> The file is downloaded, but oligo::read.celfiles() returns the following
> e...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...>
> oligo::read.celfiles("GSM907811.CEL.gz")
>
> everything works fine. (oligo is a bioConductor package)
>
> However, if I download using
>
> download.file("
>
> https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz
> ",
> destfile = "GSM907811.CEL.gz")
>
> The file is downloaded, but oligo::read.celfiles() returns the following
> error:
>
> Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
> End of gz file reached unexpected...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...uot;GSM907811.CEL.gz")
>>
>> everything works fine. (oligo is a bioConductor package)
>>
>> However, if I download using
>>
>> download.file("
>> https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&for
>> mat=file&file=GSM907811%2ECEL%2Egz
>> ",
>> destfile = "GSM907811.CEL.gz")
>>
>
> On windows, the 'mode' argument to download.file() needs to be "wb" (write
> binary) for binary files.
>
> Martin
>
>
>> The file is downloaded, but oligo...