[Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset

[Gordon K Smyth]

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 <sruddy17 at gmail.com>
> To: bioc-sig-sequencing at 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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