Hi Sean, Downloading the series file directly and running getGEO worked for me. Many thanks, Mark On Wed, Jul 7, 2010 at 5:21 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > > On Wed, Jul 7, 2010 at 12:05 PM, Mark Dunning <mark.dunning at="" 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/GSE5 350/GSE5350-GPL2507_series_matrix.txt.gz',destfile='GSE5350-GPL2507_se ries_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-G PL1355_series_matrix.txt.gz' >> Error in >> download.file(sprintf("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMa trix/%s/%s", >> ?: >> ?cannot open URL >> >> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5350/GSE5350-G PL1355_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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >