Hi, I am using the package GEOquery. But there is an error getting the GEO Series information: > gds <- getGEO("GSE2") Found 1 file(s) GSE2_series_matrix.txt.gz versuche URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2/GSE2_series_mat rix.txt.gz' ftp data connection made, file length 14773 bytes URL ge?ffnet downloaded 14 Kb Fehler in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : Zeile 1 hatte keine 5 Elemente Zus?tzlich: Warning messages: 1: In if (nchar(val) == nchar(x)) return(NA) : Bedingung hat L?nge > 1 und nur das erste Element wird benutzt 2: In if (nchar(val) == nchar(x)) return(NA) : Bedingung hat L?nge > 1 und nur das erste Element wird benutzt 3: In if (nchar(val) == nchar(x)) return(NA) : Bedingung hat L?nge > 1 und nur das erste Element wird benutzt 4: In read.table(con, sep = "\t", header = FALSE, nrows = i) : unvollst?ndige letzte Zeile von readTableHeader gefunden in 'C:\TEMP\Rtmp4xCqxE\file6df11649' > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.4.0 RCurl_0.9-3 Biobase_2.0.0 What is wrong? Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

On Mon, Jun 2, 2008 at 10:39 AM, Markus Schmidberger <schmidb at="" ibe.med.uni-muenchen.de=""> wrote: > Hi Sean, > > here is the translation: > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > > Line 1 has no 5 elements > > Additional Warnings: > 1: In if (nchar(val) == nchar(x)) return(NA) : > Condition hat length > 1 and only first element will be used > 2 : ... - same - > 3 : ... - same - > > 4: In read.table(con, sep = "\t", header = FALSE, nrows = i) : > incomplete last line in readTableHeader Thanks, Markus, for the translation. I'll have to find a windows machine on which to try this, but there could also be a character encoding issue--I have seen that before. NCBI has (I think) switched everything to UTF-8, so I haven't seen it be a problem recently. Sean > Sean Davis schrieb: >> >> 2008/6/2 Markus Schmidberger <schmidb at="" ibe.med.uni-muenchen.de="">: >> >>> >>> Hi, >>> >>> I am using the package GEOquery. >>> But there is an error getting the GEO Series information: >>> >>> >>>> >>>> gds <- getGEO("GSE2") >>>> >>> >>> Found 1 file(s) >>> GSE2_series_matrix.txt.gz >>> versuche URL >>> >>> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2/GSE2_series _matrix.txt.gz' >>> ftp data connection made, file length 14773 bytes >>> URL ge?ffnet >>> downloaded 14 Kb >>> >>> Fehler in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>> na.strings, >>> : >>> Zeile 1 hatte keine 5 Elemente >>> Zus?tzlich: Warning messages: >>> 1: In if (nchar(val) == nchar(x)) return(NA) : >>> Bedingung hat L?nge > 1 und nur das erste Element wird benutzt >>> 2: In if (nchar(val) == nchar(x)) return(NA) : >>> Bedingung hat L?nge > 1 und nur das erste Element wird benutzt >>> 3: In if (nchar(val) == nchar(x)) return(NA) : >>> Bedingung hat L?nge > 1 und nur das erste Element wird benutzt >>> 4: In read.table(con, sep = "\t", header = FALSE, nrows = i) : >>> unvollst?ndige letzte Zeile von readTableHeader gefunden in >>> 'C:\TEMP\Rtmp4xCqxE\file6df11649' >>> >>> >>> >>>> >>>> sessionInfo() >>>> >>> >>> R version 2.7.0 (2008-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> >>> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MON ETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods >>> base >>> other attached packages: >>> [1] GEOquery_2.4.0 RCurl_0.9-3 Biobase_2.0.0 >>> >>> >>> What is wrong? >>> >> >> Hi, Markus. Unfortunately, I read no German, so I can't be sure what >> the exact error is. However, I cannot reproduce the error on R 2.7.0 >> on my Mac. Perhaps it is a windows-specific problem. Could you do me >> a favor and translate the error as best you can? >> >> Thanks, >> Sean >> > > > -- > Dipl.-Tech. Math. Markus Schmidberger > > Ludwig-Maximilians-Universit?t M?nchen > IBE - Institut f?r medizinische Informationsverarbeitung, > Biometrie und Epidemiologie > Marchioninistr. 15, D-81377 Muenchen > URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] > ibe.med.uni-muenchen.de > Tel: +49 (089) 7095 - 4599 > >