On Mon, Nov 25, 2013 at 5:36 AM, Dan Du <tooyoung@gmail.com> wrote: > Hi there and Sean, > > The problem is the extra 'GPL' meta line in the full soft file, it will > confuse the built-in file parser. Maybe this could be considered a bug, > since for each GEO series (not super series) there should be only one > GPL.ID associated with it. The meta data returned after parsing the soft > file should contain only a length one GPL.ID for the platform. (CCing > Sean for a possible fix) > > > You should be able to proceed with the first line changed as follows, > #1, either retrieve at run time, preferred > gds4577 <- getGEO(GEO='GDS4577') > #2, or download the GDS4577.soft.gz instead of the full one. > gds4577 <- getGEO(filename='GDS4577.soft.gz') > > Considering the GEOquery is more an on-line tool-set to let you download > the GEO data on-the-go, it make less sense to pre-download the soft file > manually. > > Hi, Dan. Thanks for the report and diagnosis. Yes, GEOquery currently does not handle the case of the "full_soft" file, a file that is a combination of the GDS expression and the GPL information associated with the GDS. I've put parsing the full_soft format on my TODO list. For the time being, avoiding the "full_soft" file format is what I would recommend, also. Doing so is not a problem since GEOquery will reconstruct the "full_soft" file contents when importing a GDS using the standard GEOquery workflow. Sean > > Best, > Dan > > On Sun, 2013-11-24 at 20:21 +0800, 水静流深 wrote: > > hi,i am new to bioconductor,when i run the following command ,i get > wrong output > > Error in gzfile(fname, open = "rt") : invalid 'description' argument > > what is the matter? > > > > library(Biobase) library(GEOquery) gds4577 <- > getGEO(filename='c:/test/GDS4577_full.soft.gz') eset <- > GDS2eSet(gds4577, do.log2=TRUE) > eset <- GDS2eSet(gds4577, > do.log2=TRUE) File stored at: > C:\DOCUME~1\sanya\LOCALS~1\Temp\RtmpQtuak0/GPL1261.annot.gzC:\DOCUM E~1\sanya\LOCALS~1\Temp\RtmpQtuak0/GPL1261.annot.gz > Error in gzfile(fname, open = "rt") : invalid 'description' argument > In addition: Warning messages: 1: In if (GSEMatrix & geotype == > "GSE") { : the condition has length > 1 and only the first element > will be used 2: In if (geotype == "GDS") { : the condition has > length > 1 and only the first element will be used 3: In if (geotype == > "GSE" & amount == "full") { : the condition has length > 1 and only > the first element will be used 4: In if (geotype == "GSE" & amount != > "full" & amount != "table") { : the condition has length > 1 and only > the first element will be used 5: In if (geotype == "GPL"! > > ) { : the condition has length > 1 and only the first element > will be used 6: In if (!file.exists(destfile)) { : the condition > has length > 1 and only the first element will be used 7: In > download.file(myurl, destfile, mode = mode, quiet = TRUE, method = > getOption("download.file.method.GEOquery")) : only first element of > 'url' argument used 8: In download.file(myurl, destfile, mode = mode, > quiet = TRUE, method = getOption("download.file.method.GEOquery")) : > only first element of 'destfile' argument used > eset Error: object > 'eset' not found > > what is the matter with my computer? > > > sessionInfo() R version 3.0.2 (2013-09-25) Platform: > i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Chinese_People's > Republic of China.936 LC_CTYPE=Chinese_People's Republic of China.936 > [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C > [5] LC_TIME=Chinese_People's Republic of > China.936 attached base packages: [1] parallel stats graphics > grDevices utils datasets methods base other attached packages: > [1] GEOquery_2.28.0 BiocInstaller_1.12.0 affy_1.40.0 > Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not > attached): [1] affyio_1.30.0 preprocessCore_1.24.0 RCurl_1.95-4.1 > tools_3.0.2 > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]