small RNA differential expression analysis

Question

[rrsowmya]

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

[Devon Ryan]

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

Answer 1

[GouthamAtla]

Deseq Question - Input Normalized Read Counts

Answer 2

[rrsowmya]

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

[GouthamAtla]

1. A simple correlation coefficient or PCA.
2. DESeq/DESe2 vignette

[Devon Ryan]

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.