On Sun, Jul 27, 2008 at 11:44 PM, Gad Abraham <gabraham at="" csse.unimelb.edu.au=""> wrote: > Hi, > > I'm using GEOquery 2.4.1 to read an NCBI GEO file > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_ser ies_matrix.txt.gz > but parseGEO throws an error. The switch argument evaluates to "0", which > doesn't match alternative, so it tries to match on the last empty argument > and fails. I don't know if this is related to the warnings; the file > contains text such as manufacturer\xa1\xafs which may not parse correctly. > > Below is the output. > > Thanks for any advice, > Gad > >> g <- getGEO(filename="GSE4284_series_matrix.txt") Hi, Gad. The filename argument does not yet take GSE series matrix files as an argument. I have a couple of changes to make with GSE series matrix handling and adding file-based parsing is one of them. Sean

Sean Davis wrote: > On Sun, Jul 27, 2008 at 11:44 PM, Gad Abraham > <gabraham at="" csse.unimelb.edu.au=""> wrote: >> Hi, >> >> I'm using GEOquery 2.4.1 to read an NCBI GEO file >> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_se ries_matrix.txt.gz >> but parseGEO throws an error. The switch argument evaluates to "0", which >> doesn't match alternative, so it tries to match on the last empty argument >> and fails. I don't know if this is related to the warnings; the file >> contains text such as manufacturer\xa1\xafs which may not parse correctly. >> >> Below is the output. >> >> Thanks for any advice, >> Gad >> >>> g <- getGEO(filename="GSE4284_series_matrix.txt") > > Hi, Gad. The filename argument does not yet take GSE series matrix > files as an argument. I have a couple of changes to make with GSE > series matrix handling and adding file-based parsing is one of them. > > Sean Hi Sean, Is this also the reason for scan() failing when using the GEO name instead of the filename? (See below) Thanks, Gad > g <- getGEO("GSE4284") Found 1 file(s) GSE4284_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_seri es_matrix.txt.gz' ftp data connection made, file length 4137302 bytes opened URL ================================================== downloaded 3.9 Mb Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got '"Schizosaccharomycespombe"' In addition: Warning message: In grep("^!Sample_", a, ignore.case = TRUE) : input string 1 is invalid in this locale > sessionInfo() R version 2.7.1 (2008-06-23) x86_64-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.4.1 RCurl_0.9-4 Biobase_2.0.1 -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham