Question: Getting dChip SNP intensity in BioC?
0
gravatar for Jeff Gentry
11.1 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
Hi there ... I'm probably just overlooking something obvious, but I didn't see this in the oligo package. I was hoping to be able to generate the signal values for samples in SNP datasets in the same manner as dChip & genepattern do. As an example, the Genepattern .SNP file format each sample has both an intensity and a call column. Thanks -J
snp oligo • 634 views
ADD COMMENTlink modified 11.1 years ago by Henrik Bengtsson2.4k • written 11.1 years ago by Jeff Gentry3.9k
Answer: Getting dChip SNP intensity in BioC?
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gravatar for Henrik Bengtsson
11.1 years ago by
United States
Henrik Bengtsson2.4k wrote:
Hi, see recent BioC thread 'dChip LOH and copy number analysis' on Sept 17, 2008: https://stat.ethz.ch/pipermail/bioconductor/2008-September/024208.html Could be what you are looking for. /Henrik On Thu, Sep 25, 2008 at 12:25 PM, Jeff Gentry <jgentry at="" jimmy.harvard.edu=""> wrote: > Hi there ... > > I'm probably just overlooking something obvious, but I didn't see this in > the oligo package. I was hoping to be able to generate the signal > values for samples in SNP datasets in the same manner as dChip & > genepattern do. As an example, the Genepattern .SNP file format each > sample has both an intensity and a call column. > > Thanks > -J > > _______________________________________________ > 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 >
ADD COMMENTlink written 11.1 years ago by Henrik Bengtsson2.4k
> 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.
ADD REPLYlink written 11.1 years ago by Jeff Gentry3.9k
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