Hi, I'm using getGEO to obtain the serie GSE18154 and I encounter the following error: > gse18154 <- getGEO("GSE18154") Found 1 file(s) GSE18154_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE18154/GSE18154_ser ies_matrix.txt.gz ' ftp data connection made, file length 1891349 bytes opened URL downloaded 1.8 Mb Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got '"GSM453789"' In addition: Warning messages: 1: In grepl("^!Series_", dat) : input string 38 is invalid in this locale 2: In grepl("^!Series_", dat) : input string 46 is invalid in this locale 3: In grepl("^!Sample_", dat) : input string 38 is invalid in this locale 4: In grepl("^!Sample_", dat) : input string 46 is invalid in this locale I think part of the problem may be the extra quotation marks (when comparing to another matrix file that works), after downloading it and manually removing the quotation marks, getGEO load the local file with less warnings: > gse18154 <- getGEO(filename="GSE17308_series_matrix.txt") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got 'GSM433039' Timothy [[alternative HTML version deleted]]

On Fri, May 28, 2010 at 4:56 AM, Timothy Wu <2huggie@gmail.com> wrote: > Hi, > > I'm using getGEO to obtain the serie GSE18154 and I encounter the following > error: > > > gse18154 <- getGEO("GSE18154") > Found 1 file(s) > GSE18154_series_matrix.txt.gz > trying URL ' > > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE18154/GSE18154_s eries_matrix.txt.gz > ' > ftp data connection made, file length 1891349 bytes > opened URL > downloaded 1.8 Mb > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > scan() expected 'a real', got '"GSM453789"' > In addition: Warning messages: > 1: In grepl("^!Series_", dat) : input string 38 is invalid in this locale > 2: In grepl("^!Series_", dat) : input string 46 is invalid in this locale > 3: In grepl("^!Sample_", dat) : input string 38 is invalid in this locale > 4: In grepl("^!Sample_", dat) : input string 46 is invalid in this locale > > I think part of the problem may be the extra quotation marks (when > comparing > to another matrix file that works), after downloading it and manually > removing the quotation marks, getGEO load the local file with less > warnings: > > > gse18154 <- getGEO(filename="GSE17308_series_matrix.txt") > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > scan() expected 'a real', got 'GSM433039' > > Hi, Timothy. It is hard to comment without sessionInfo(), but my guess is that this has to do with the locale you are using. Your code works fine for me. Check the locale and perhaps change it to "C" locale or "en_US" (the exact terminology depends a bit on OS). See the help for "locales" for details. Sean > library(GEOquery) > gse = getGEO("GSE18154") Found 1 file(s) GSE18154_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE18154/GSE18154_ser ies_matrix.txt.gz ' ftp data connection made, file length 1891349 bytes opened URL ================================================== downloaded 1.8 Mb File stored at: /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//RtmpSCXRVm/GPL9216. soft > sessionInfo() R version 2.12.0 Under development (unstable) (2010-04-30 r51866) i386-apple-darwin9.8.0 locale: [1] en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GEOquery_2.13.0 RCurl_1.4-1 bitops_1.0-4.1 Biobase_2.9.0 loaded via a namespace (and not attached): [1] tools_2.12.0 [[alternative HTML version deleted]]