[BioC] Getting dChip SNP intensity in BioC?

Jeff Gentry jgentry at jimmy.harvard.edu
Thu Sep 25 22:46:14 CEST 2008


> Could be what you are looking for.

There's some good info in there, thanks!  This isn't quite what I'm after
right now though, I'm trying to go in the other direction - exporting data
from a BioC session into a file to read into dChip & genepattern (their
formats are similar for SNP data, information on GP's .SNP file format
is available
here: http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_fileformats_text.html#snp).


I know how to generate the SnpCallSet object to get the call information,
but both of these programs also want the signal intensity data to go along
w/ that, which is what I don't know how to get at within BioC.



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