[BioC] GEOquery and GSE error

[Ovokeraye Achinike-Oduaran]

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-GPL96_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE9006/GSE9006-GPL96_series_matrix.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