[BioC] How to use GEOquery to extract more than the default information from a GSE

Manca Marco (PATH) m.manca at path.unimaas.nl
Fri Jul 24 15:11:50 CEST 2009

Dear Sean and dear bioconductors,

I am writing you to ask a source of inspiration (code pieces, notes, references, whatever you might think appropriate) to import array annotation and other data from the GSE I am trying to work with (namely the GSE9820) into my eset.

I have read on GEOquery's vignette that this is actually possible, despite being a bit tricky:

"So, using a combination of lapply on the GSMList, one can extract as many columns of interest as necessary to build the data structure of choice. Because the GSM data from the GEO website are fully downloaded and included in the GSE object, one can extract foreground and background as well as quality for two-channel arrays, for example. Getting array annotation is also a bit more complicated, but by replacing \platform" in the lapply call to get platform information for each array, one can get other information associated with each array. Future work with this package will likely focus on better tools for manipulating GSE data" From http://www.bioconductor.org/packages/2.4/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf Page 22 of 22

...but I can't find anywhere any hint.

Thank you in advance for your patience and support.

My best regards,

Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
E-mail: m.manca at path.unimaas.nl
Mobile: +31626441205
Twitter: @markomanka

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