[BioC] GEOquery error

[James W. MacDonald]

Hi Sean,

 > geoq <- getGEO("GSE9514")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/
Found 1 file(s)
GSE9514_series_matrix.txt.gz
   % Total    % Received % Xferd  Average Speed   Time    Time Time  Current
                                  Dload  Upload   Total   Spent Left  Speed
100  378k  100  378k    0     0   204k      0  0:00:01  0:00:01 
--:--:--  204k
File stored at:
/data3/tmp/RtmpkDXZzR/GPL90.soft
Error in xj[i] : only 0's may be mixed with negative subscripts

And the error appears to come from this section in parseGPL():

if (hasDataTable) {
         nLinesToRead <- NULL
         if (!is.null(n)) {
             nLinesToRead <- n - length(txt)
         }
         dat3 <- fastTabRead(con, n = nLinesToRead, quote = "")
         geoDataTable <- new("GEODataTable", columns = cols, table = 
dat3[1:(nrow(dat3) -
             1), ])
     }

Where there is no error trapping for the case that fastTabRead returns a 
zero row data.frame:

debug: dat3 <- fastTabRead(con, n = nLinesToRead, quote = "")
Browse[3]> dim(dat3)
[1]  0 17
Browse[3]> dat3
  [1] ID ORF
  [3] SPOT_ID                          Species Scientific Name
  [5] Annotation Date                  Sequence Type
  [7] Sequence Source                  Target Description
  [9] Representative Public ID         Gene Title
[11] Gene Symbol ENTREZ_GENE_ID
[13] RefSeq Transcript ID             SGD accession number
[15] Gene Ontology Biological Process Gene Ontology Cellular Component
[17] Gene Ontology Molecular Function
<0 rows> (or 0-length row.names)

Best,

Jim

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099