Deseq2 within samples variability
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sally_b86 • 0
@sally_b86-13975
Last seen 5.4 years ago

Hello, 

Is there a way to correct for within sample variability?? PCA plot show that some replicates within some samples have higher variability than others? Does this affect alot the DEG output? And is it possible to avoid this other than removing highly variable samples?

Thank you

 

within variability samples deseq2 • 701 views
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@mikelove
Last seen 23 hours ago
United States

The variability among samples is a critical part of the model. If the differences across condition are not larger than the differences among biological replicates, this is important information coming from the experiment. I would not remove the highly variable samples unless these are failing QC (e.g. check the FASTQC reports in MultiQC).

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