This follows on from a question from Saurin D. Jani, on the list a year ago: https://stat.ethz.ch/pipermail/bioconductor/2005-January/007405.html A working example: library(AnnBuilder) geo <- GEO() queryGEO(geo,"GSM107") This downloads and parses:- http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM107&targ=self&for m=text&view=data This fails for GEO Datasets (GDS files) like GDS813 (Saurin's example) because the URL isn't accepted - the NCBI returns an HTML page which redirects you to: http://www.ncbi.nlm.nih.gov/projects/geo/gds/gds_browse.cgi?gds=813 This page in turn can be used (by a human, a little more tricky in code) to download the actual GDS file - but only in compressed form: ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS813.soft.gz What this means is that at the moment, queryGEO doesn't support GDS files. Even if it did, they are generally large and only available in compressed format, making things generally more complicated. Would it make more sense to provide to separate functions: Firstly, to download the file (dealing with all possible URLs) and if need be decompress it. Secondly, to parse a GEO file from the provided handle/filename/url This makes sense for other large GEO files like the GPL annotation files, as well as the GEO datasets (GDS files). It seems wasteful and slow to download them fresh each time. Peter

Peter, I have recently uploaded a new package to bioconductor called GEOquery. It is available as a development package (http://www.bioconductor.org/packages/bioc/1.8/html/GEOquery.html), but it doesn't depend on much, so should work with recent R and bioconductor releases. It is capable of downloading and parsing GDS, GSM, GPL, and GSE. (GSE download and parsing seems to be broken on windows, at least for some GSEs--working on that). After installing, you could do: > library(GEOquery) # the following takes about a minute or so.... > gds813 <- getGEO('GDS813') And then to convert to an exprSet, simply do: > eset <- GDS2eSet(GDS,do.log2=TRUE) > eset Expression Set (exprSet) with 22690 genes 20 samples phenoData object with 4 variables and 38 cases varLabels : sample : disease.state : tissue : description Sean On 1/4/06 10:27 AM, "Peter" <bioconductor-mailinglist at="" maubp.freeserve.co.uk=""> wrote: > This follows on from a question from Saurin D. Jani, on the list a year ago: > > https://stat.ethz.ch/pipermail/bioconductor/2005-January/007405.html > > A working example: > > library(AnnBuilder) > geo <- GEO() > queryGEO(geo,"GSM107") > > This downloads and parses:- > > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM107&targ=self&f orm=text&v > iew=data > > This fails for GEO Datasets (GDS files) like GDS813 (Saurin's example) > because the URL isn't accepted - the NCBI returns an HTML page which > redirects you to: > > http://www.ncbi.nlm.nih.gov/projects/geo/gds/gds_browse.cgi?gds=813 > > This page in turn can be used (by a human, a little more tricky in code) > to download the actual GDS file - but only in compressed form: > > ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS813.soft.gz > > What this means is that at the moment, queryGEO doesn't support GDS > files. Even if it did, they are generally large and only available in > compressed format, making things generally more complicated. > > Would it make more sense to provide to separate functions: > > Firstly, to download the file (dealing with all possible URLs) and if > need be decompress it. > > Secondly, to parse a GEO file from the provided handle/filename/url > > This makes sense for other large GEO files like the GPL annotation > files, as well as the GEO datasets (GDS files). It seems wasteful and > slow to download them fresh each time. > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor