[BioC] Retrieving MAQC data from GEO using GEOquery

[James F. Reid]

Hi Mark,

I have observed the same thing happening using other GEO datasets.
The solution that worked for me (and I don't really know why) was to 
force download.file to use 'wget' on my system by setting
options(download.file.method="wget")

HTH.
J.

On 07/07/2010 06:05 PM, Mark Dunning 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).
>
>> 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'
>
>
> I tried using the GSElimits parameter but it still persists in trying
> to download all the data.
>
> 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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