On Wed, Jul 7, 2010 at 12:05 PM, Mark Dunning <mark.dunning@gmail.com>wrote:

> Hi,
>
> I am trying to retrieve the MAQC arrays from GEO. However I am only
> interested in the arrays that were run on Illumina and the dataset
> contains 19 different platforms. Is there a way of specifying which
> platform I want to retrieve? The getGEO command seems to fail on the
> first platform in the series and never gets to the one I'm interested
> in (GPL2507).
>

Hi, Mark.  I really should support this use case directly, but I don't have
the syntactic sugar in place to do so right now.  It is on the TODO list,
though.  However, what you want to do is pretty simple to do directly:

download.file('
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5350/GSE5350-GPL2507_series_matrix.txt.gz
',destfile='GSE5350-GPL2507_series_matrix.txt.gz')

gse = getGEO(filename=GSE5350-GPL2507_series_matrix.txt.gz")


> >library(GEOquery)
> >temp = getGEO(GEO="GSE5350", GSEMatrix=TRUE, GSElimits=c(127,150))
> Found 19 file(s)
> GSE5350-GPL1355_series_matrix.txt.gz
> trying URL '
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5350/GSE5350-GPL1355_series_matrix.txt.gz
> '
> Error in download.file(sprintf("
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s",
>  :
>  cannot open URL
> '
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5350/GSE5350-GPL1355_series_matrix.txt.gz
> '
>
>
This error is intermittent and is on the NCBI end.  I get this on a pretty
regular basis.  Try back in a few minutes and it will probably work.


>
> I tried using the GSElimits parameter but it still persists in trying
> to download all the data.
>
>
Unfortunately, GSElimits only apply to a full SOFT format download
(GSEMatrix=FALSE).  There is not an easy way to use GSElimits when
GSEMatrix=TRUE since there are multiple files involved.

Sean



> Cheers,
>
> Mark
>
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.12.0 RCurl_1.4-2     bitops_1.0-4.1  Biobase_2.8.0
>
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