<p>Hi,</p>

<p>I may have a silly question. How should I get normalized counts from DESeq2? If I understand it right, rlog and vst are both normalized counts which one is better? or Should I just use &quot;counts(dds,normalized=TRUE)&quot; instead of rlog or vst. Thank you.</p>

<p>-X</p>

<p>For things like calculating fold-changes, one would normally use the output of <code>count(dds, normalized=T)</code>. The other two you mentioned and so much count but rather transformed counts. These are useful for things like making a heatmap, or PCA, or anything that involves clustering/imaging.</p>

<p>BTW, none of these will give you the same fold-change that DESeq2 does, because you&#39;re not using a prior distribution.</p>
