Geoquery And Gse Error

Question

[Avoks]

Hi all,

I am unable to access a series file even though I get a message that it saved to a local directory, albeit with an error message and a number of warnings, after retrieval with GEOquery. Any ideas as to what I may be doing wrong?

Thanks.

Avoks

gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) Found 2 file(s) GSE9006-GPL96seriesmatrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE9006/GSE9006-GPL96seriesmatrix.txt.gz' ftp data connection made, file length 5775933 bytes opened URL downloaded 5.5 Mb

File stored at: C:...\Temp\RtmpJM0ZOp/GPL96.soft Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData In addition: Warning messages: 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : seek on a gzfile connection returned an internal error 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : seek on a gzfile connection returned an internal error 3: In readLines(con, 1) : seek on a gzfile connection returned an internal error 4: In read.table(file = file, header = header, sep = sep, quote = quote, : seek on a gzfile connection returned an internal error 5: In read.table(file = file, header = header, sep = sep, quote = quote, : seek on a gzfile connection returned an internal error 6: In read.table(file = file, header = header, sep = sep, quote = quote, : seek on a gzfile connection returned an internal error 7: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist

gse9006 Error: object 'gse9006' not found

show(gse9006) Error in show(gse9006) : error in evaluating the argument 'object' in selecting a method for function 'show': Error: object 'gse9006' not found

This question is also being asked on BioC. @Khader: Not quite sure how to link it across.

Answer 1

[Sean Davis]

As with all questions related to R/Bioconductor, always include the output of sessionInfo() so that potential responders can see versions of packages. In this case, I believe the GEOquery package needs to be at least version 2.19.4 since 2.19.3 contains a bug (noted above), so I suggest an update to the package.

The relevant email thread on the Bioconductor email list is:

http://article.gmane.org/gmane.science.biology.informatics.conductor/36696