On Mon, May 25, 2009 at 5:00 PM, Wacek Kusnierczyk <
Waclaw.Marcin.Kusnierczyk@idi.ntnu.no> wrote:

> Wolfgang Huber wrote:
> >
> > Dear Wacek,
> >
> > thank you for the feedback and pointing this out. Two general remarks:
>
> thank you for the response.
>
> >
> > 1. Please include a reproducible example (R script) for others to
> > reproduce your experience, and subsequently the output of sessionInfo().
>
> a reproducible (on my machine, at least) example is as follows:
>
>    library(GEOquery)
>    repeat {
>       filename = getGEOfile('GSE13638')
>       if (!is.null(filename)) break }
>    system.time({gse13638 = getGEO(filename=filename)})
>    # elapsed: 620
>
> (so it was 'faster' this time, only 10 minutes...)
>
> session info is as follows:
>
> R version 2.10.0 Under development (unstable) (2009-05-25 r48607)
> i686-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.9.0 RCurl_0.94-1   Biobase_2.5.2
>
>
>
> >
> > 2. Robert Gentleman's book "R Programming for Bioinformatics" (as well
> > as many free sources on the web) describes how to profile R code in
> > order to see in which functions the CPU time is spent. Based on this,
> > you can investigate where to invest developer time for improving the
> > code.
>
> yes, i know;  but i thought someone could already have done this or have
> a hint anyway, as this does not seem likely to be just my local
> problem.  before i spend too much time on a potentially well-known
> issue, it's surely fine to ask others, including the developer.
>

Thanks, Wacek, for the report.  This is a known issue and GEOquery could
probably be smarter than it currently is; I have not changed that code in q
while since GEO began using GSE Matrix files.  You could try using
GSEMatrix=TRUE, as the documentation suggests.  You will find that will deal
with your speed issues.

Sean

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