Question: Error using GEOquery
0
gravatar for Markus Schmidberger
11.5 years ago by
Markus Schmidberger380 wrote:
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
geoquery • 889 views
ADD COMMENTlink modified 11.5 years ago by Sean Davis21k • written 11.5 years ago by Markus Schmidberger380
Answer: Error using GEOquery
0
gravatar for Sean Davis
11.5 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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 > >
ADD COMMENTlink written 11.5 years ago by Sean Davis21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 138 users visited in the last hour