Using DESeq2 only for normalization
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phmai1148 • 0
@a0d449cd
Last seen 4 weeks ago
United States

I have raw miRNA seq count data that I want to normalize using deseq normalization. I will export the data after normalization to conduct the downstream analysis (I will not use deseq2 package to conduct the differential analysis). In this case:

  1. Do I have to use the (vst) function or just use (counts, normalized=TRUE) and (normTransform, f=log2, pc=1)?
  2. Do I have to collapse the technical replicates using the (collapseReplicates) function before or after the deseq normalization?
  3. I also want to filter miRNAs based on a specific minimum number of counts in a minimum number of samples (e.g keep only those miRNAs with a minimum count of 10 in at least 30% of the samples). Do I have to do this filtering step before or after deseq normalization?
DESeq2 Normalization • 462 views
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ATpoint ★ 3.8k
@atpoint-13662
Last seen 1 day ago
Germany

I have answered all this already DESeq Normalization and miRNAs Filtering

It's bad practice to open duplicate questions. Add comments to the previous one if anything is unclear or answers are not sufficient.

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