[BioC] DESeq nbinomGLMTest specific comparisons

[James Floyd]

Hi,

Thanks for your reply, and sorry for the delay. As always, I got
distracted by other projects Š

I am looking to perform a DE analysis for a disease with three states,
while correcting for smoking status. So I was using Š :

fit0 = fitNbinomGLMs( cdsFull, count ~ smoking )
fit1 = fitNbinomGLMs( cdsFull, count ~ smoking + condition )

Š then comparing the models to see whether adding condition improves the
fit of the model and has a significant effect (as described in the
vignette).


However, if I wanted to make a specific comparison of, say, the two most
extreme disease states (state A against C, ignoring B), how would I go
about doing this?

Thanks for letting me know about DESeq2, I was unaware of it.

Cheers,
Jamie



On 27/11/2013 17:21, "Steve Lianoglou" <lianoglou.steve at gene.com> wrote:

>Hi,
>
>On Tue, Nov 26, 2013 at 8:21 AM, James Floyd <j.a.floyd at qmul.ac.uk> wrote:
>> Hi,
>>
>> I notice in the DESeq
>>vignette<http://bioconductor.org/packages/release/bioc/vignettes/DESeq/in
>>st/doc/DESeq.pdf> there is a "Fixme" comment about including how to test
>>specific comparisons using nbinomGLMTest (page 12). It would be great if
>>someone with experience doing this could let me know how it is done.
>
>Can you be more specific of what you'd like to test? Perhaps you can
>setup your problem for us and point out what particular comparison
>you'd like to make, and someone can help you better.
>
>Furthermore, if you are using DESeq, you might consider shifting over
>to DESeq2. It offers a number of benefits over DESeq, and (I believe)
>this is where the DESeq authors are focussing the lion's share of
>their attention anyhow.
>
>-steve
>
>-- 
>Steve Lianoglou
>Computational Biologist
>Genentech