On Fri, Dec 17, 2010 at 8:28 AM, James F. Reid <
james.reid@ifom-ieo-campus.it> wrote:

> Dear list,
>
> I can't seem to get the GSElimits parameters of the GEOquery getGEO
> function to work, it seems to be ignored as the full dataset is always
> returned.
>
>
Thanks, James, for the very clear report of the problem.  I have fixed this
in both the Release (v2.16.2) and Devel branches (v2.17.2).  The changes
should move through the build system in a day or two.

Sean


> Many thanks.
> James.
>
> library("GEOquery")
>
> softFile <- system.file("extdata/GSE781_family.soft.gz", package =
> "GEOquery")
>
> ## full set
> gse <- getGEO(filename = softFile)
> Parsing....
> Found 36 entities...
> GPL96 (1 of 36 entities)
> GPL97 (2 of 36 entities)
> GSM11805 (3 of 36 entities)
> etc..
>
> ## reduced set (samples 1 to 5)
> gseSub <- getGEO(filename = softFile, GSElimits = c(1, 5))
> Parsing....
> Found 36 entities...
> GPL96 (1 of 36 entities)
> GPL97 (2 of 36 entities)
> GSM11805 (3 of 36 entities)
> etc..
>
>
> length(names(GSMList(gse)))
> [1] 34
> length(names(GSMList(gseSub)))
> [1] 34
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  tools     methods
> [8] base
>
> other attached packages:
> [1] GEOquery_2.16.1 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.5-0 XML_3.2-0
>
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