Hi Gordon,

Thanks for the response. One of my data sets has 8 conditions and no
replicates and so I wanted to emulate DESeq's way of pooling the samples and
also use an offset matrix. I was hoping to avoid doing it manually so that I
don't mess it up. I could do this all in edgeR and pool the samples but I'm
not sure how well this would work under edgeR vs. DESeq. I am curious though
what sounds off to you in my previous email. I don't feel entirely
comfortable doing this manually but hopefully it's just because I left out
some details. I was trying to follow the DESeq method and the only
difference I saw was in the size factor calculations which I changed for my
own needs by using the offset values for each tag and sample.

I appreciate the help!

Best,
Sean

On Fri, Jul 15, 2011 at 12:02 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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@gmail.com>
>> To: bioc-sig-sequencing@r-project.**org<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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