I am using variance stabilizing transformation on my rna seq count data with Deseq2.
Do I need to use quantile normalize the samples or does variance stabilizing transformation function take care of it?
Thanks, I just wanted to make sure that genes that have "low" counts in two samples are comparable (i.e. have similar rank for example).
Yes, the counts are comparable after normalization and transformation.
What would be the reason for quantile normalization, beyond the sequencing depth normalization we already implement?
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