[BioC] DESeq2: Paired Test
anders at embl.de
Wed Apr 16 22:47:48 CEST 2014
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.
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