[BioC] snarfing GEO datasets...

[Vincent J. Carey, Jr.]

in package annotate there is GEOAnno, a first pass
at this application for GEO annotation of platforms

arguments are

platform (a string that identifies the platform in the
GEO catalog)

massageStruct (a list with elements keepIndsExpr,
ncols, header, pad, stripCols -- self explanatory?
the idea is that they give you a ragged table, you
can find the regimented subtable (with common column
number ncols) in rows given by keepIndsExpr), state
the header titles you want, and do something with
"," as last token and omit columns you don't need)

inURL (where do you go to look at GEO datasets)

the massage struct is the diciest part, but examples
exist for GPL80 (HUGeneFL) and GPL91 (U95A) -- all
in the annotate package under GEOAnno 
-- 
---
Vince Carey, PhD
Ass't Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA

stvjc@channing.harvard.edu

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