Hi Sean,
I'm curious to know why not use edgeR, since edgeR does what you want and
DESeq doesn't?
I might be wrong, but the manual analysis that you describe doesn't sound
right.
Best wishes
Gordon
Date: Thu, 14 Jul 2011 12:54:49 -0700
From: Sean Ruddy <srudd...@gmail.com>
To: bioc-sig-sequencing@r-project.org
Subject: [Bioc-sig-seq] Supplying own variance functions and adjusted
counts to a DESeq dataset
Hi,
I have a RNA-Seq count data set that requires separate offset values for
each tag and sample. DESeq does not appear to take a matrix of offset values
(unlike edgeR) in any of its functions so I've carried out the analysis
manually, ie. calculating a size factor for each tag of each sample,
adjusting the counts, then proceeding to calculate means and variances of
the adjusted counts, and finally fitting a curve for each condition to the
mean-var plot using locfit().
Essentially, I'd like to put these variance functions (or at least all the
predicted variances) and adjusted counts inside a DESeq object so that I can
take advantage of the other functions DESeq offers, tests, plots, etc...
Thanks for the help!
Sean
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