[BioC] Error in gzfile(fname, open = “rt”) : invalid 'description' argument - GEOquery

[Dan Du]

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.


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:\DOCUME~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]]
> 
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