Check variance stabilization transformation ?

Question

[debitboro]

Hi all biostars,

How can check if the variance stabilization transformation has worked well ? I've used the function getVarianceStabilizedData() of DESeq2 package as a VST method on RNASeq expression matrix, and now I want to check if the method has worked well or not ?

Any idea !

Thanks in advance

Answer 1

[swbarnes2]

if vst is your variance stabilization transformation object, "assay(vst)" will return the rows and columns of gene counts per sample, transformed. That's probably what you want to look at, if you wnat to eyeball the new values.