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small RNA differential expression analysis

I would like to know if there is any way of entering normalized count table directly into DESeq? I cannot enter the raw data since my file parsed through several layers of annotation and filtering.

Thank you

rna-seq rna-seq next-gen
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updated by Ram Ram • written by rrsowmya • rrsowmya

Short answer: no, trying to enter normalized data is wrong.

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written by Devon Ryan Devon Ryan

2 answers

Deseq Question - Input Normalized Read Counts

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written by GouthamAtla GouthamAtla

Thank you very much.

Since I'm still new to this - what statistical tests could I run to

  1. test for significance between my 3 biological replicates for each treatment.
  2. look for differential expression between treatments
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updated by Ram Ram • written by rrsowmya • rrsowmya
  1. A simple correlation coefficient or PCA.
  2. DESeq/DESe2 vignette
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updated by Ram Ram • written by GouthamAtla GouthamAtla
  1. If you can't get around using normalized counts, then limma after using voom(). Apparently edgeR is now considered OK in some circumstances, but this will depend on the nature of the counts.
  2. See above, you may want contrasts.
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updated by Ram Ram • written by Devon Ryan Devon Ryan

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