This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Check variance stabilization transformation ?

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

rna-seq variance stabilization deseq2
• 1,545 views • link
updated by swbarnes2 swbarnes2 • written by debitboro debitboro

1 answer

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.

• 1 views • link
written by swbarnes2 swbarnes2

Log in to answer this question.

More posts like this