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Error in read.affybatch

Hi I'm working GSE55945 and got an unexpected error in ReadAffy command I'll be very thankful if anyone can help me in solving it.

gse55945preset=ReadAffy(filenames = celFiles)

Error:

Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  : 
  It appears that the file GSE55945/GSM1348937_110807_HGU133_PLUS_2.0_MS_36A6.CEL.gz is corrupted.

What does this error means??

r affy limma read.affy bioconductor
• 4,519 views • link
updated by Sean Davis Sean Davis • written by 786 786

Isn't it pretty self-explanatory? Maybe you want to set compress=T in your call to ReadAffy

• 1 views • link
written by fanli.gcb fanli.gcb

I just don't understand what do you mean by compress=T??

• 1 views • link
written by 786 786

Try gse55945preset=ReadAffy(filenames = celFiles, compress=T). Alternatively, have you checked to see that your GSE dataset was downloaded completely?

• 1 views • link
written by fanli.gcb fanli.gcb

Again I got same error.

• 1 views • link
written by 786 786 
> gse55945dat = getGEO('GSE55945') 
Found 1 file(s)
GSE55945_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE55945/GSE55945_series_matrix.txt.gz'
ftp data connection made, file length 5308134 bytes
opened URL
downloaded 5.1 Mb

File stored at: 
C:\Users\NADAMU~1\AppData\Local\Temp\RtmpYF0Xxe/GPL570.soft
> gse55945raw= getGEOSuppFiles('GSE55945')
[1] "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945/"
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945//GSE55945_RAW.tar'
ftp data connection made, file length 101591040 bytes
opened URL
downloaded 51.7 Mb

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945//filelist.txt'
ftp data connection made, file length 1909 bytes
opened URL
downloaded 1909 bytes

Warning message:
In download.file(file.path(url, i), destfile = file.path(storedir,  :
  downloaded length 54234592 != reported length 101591040
> gse55945raw= getGEOSuppFiles('GSE55945')
[1] "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945/"
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945//GSE55945_RAW.tar'
ftp data connection made, file length 101591040 bytes
opened URL
downloaded 3.0 Mb

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945//filelist.txt'
ftp data connection made, file length 1909 bytes
opened URL
downloaded 1909 bytes

Warning messages:
1: In dir.create(GEO) : 'GSE55945' already exists
2: In download.file(file.path(url, i), destfile = file.path(storedir,  :
  downloaded length 3156928 != reported length 101591040
> gse55945raw= getGEOSuppFiles('GSE55945')
[1] "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945/"
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945//GSE55945_RAW.tar'
ftp data connection made, file length 101591040 bytes
opened URL
downloaded 96.9 Mb

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE55945//filelist.txt'
ftp data connection made, file length 1909 bytes
opened URL
downloaded 1909 bytes

Warning message:
In dir.create(GEO) : 'GSE55945' already exists
> tarfile <- grep("\\.tar$",rownames(gse55945raw),value = TRUE)
> untar(tarfile, exdir="GSE55945")
> celFiles <- unlist(list.files("GSE55945",pattern="\\.CEL.gz",full.names=TRUE))
> gse55945preset=ReadAffy(filenames = celFiles)
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  : 
  It appears that the file GSE55945/GSM1348937_110807_HGU133_PLUS_2.0_MS_36A6.CEL.gz is corrupted.
> gse55945preset=ReadAffy(filenames = celFiles, compress=T)
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  : 
  It appears that the file GSE55945/GSM1348937_110807_HGU133_PLUS_2.0_MS_36A6.CEL.gz is corrupted.
• 1 views • link
written by 786 786

1 answer

I can confirm this error. I'd suggest writing to NCBI GEO to see if they can confirm it as well. As the error message implies, the file appears to be corrupt. In the short term, I'd suggest simply excluding that file from analysis and move on.

• 1 views • link
written by Sean Davis Sean Davis

Thank you so much for your help

• 1 views • link
written by 786 786

If you get a resolution, let us know. It may help folks in the future with similar problems.

• 1 views • link
written by Sean Davis Sean Davis

Did you mean I should exclude only this file GSE55945/GSM1348937_110807_HGU133_PLUS_2.0_MS_36A6.CEL.gz or to exclude GSE55945???

• 1 views • link
written by 786 786

Just the "bad" file(s), not the entire directory.

• 1 views • link
written by Sean Davis Sean Davis

And if I del them than would it affect my results??

• 1 views • link
written by 786 786

I had deleted the bad files from my directory and got the results.

• 1 views • link
written by 786 786

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