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:\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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