[BioC] Retrieving MAQC data from GEO using GEOquery

[Mark Dunning]

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