Hi!

I have calculated the log fold change values for RNA-Seq Data and would like to estimate the significance of the results. I know DESeq does it already, but I want to do it manually after having normalised the counts with RPKM.

Some ideas?

Thanks in advance
<p>Assuming you&#39;ve truly done all of the required normalization, then you could just use a T-test or ANOVA (or other applicable linear model). Remember that you&#39;ll have lower power than a method like DESeq2 or edgeR since you&#39;ll not be using information sharing, but that&#39;s the simple manual route.</p>

<p>BTW, why do you want to do this? The various count-based packages are pretty nice and it&#39;s usually not a good idea to reinvent the wheel unless you have a good reason.</p>
