[BioC] DESeq2: Paired Test

[Simon Anders]

Hi Pankaj

On 16.04.2014 21:59, Pankaj Agarwal wrote:
> I followed the vignette for the section on htseq-count and your suggestion as best as I could and got some results.
> But I am not sure if I did everything right, so I would really appreciate if you could verify if the following steps is the correct way to analyze this data set:

They all look correct.

> I did not get the normalization factors in the output, whereas it does show up in the results in the vignette, so I am not sure if I missed some step.

Just type "sizeFactors(dds)" to see them.

> Also, would you expect to get meaningful results with just two matched pairs of samples with this analysis?  I am wondering if it is better to just report the FC rather than the p-values.

That depends a lot on the biology and the treatment of the samples. You 
would need to tell us much more.

In general, you should disregard genes without significant adjusted p 
values even if they have seemingly strong fold changes. On the other 
hand, if you have very many genes with significant adjusted p values, 
then you will find the most interesting among these not by looking for 
the smallest p value but rather by looking for the strongest (shrunken) 
fold changes. See our preprint for more on this.

   Simon