Question: DESeq2 p-value histogram
gravatar for reuben.schndr123
6 months ago by
reuben.schndr1230 wrote:

Hi there, Working on an assignment on RNA-seq DE analysis and I've got a couple of questions...

My Data:

  • 2 Mapped reads of Metastatic lymphoma cells (One had about a gigabyte of difference between forward and reverse reads) (n=3)
  • 3 Mapped reads of non-metastatic lymphoma cells (n=3)
  • One control sample from a normal cell for each patient (n=6)

My input for DESeq2:

  • Three-levelled primary factor "Cell_type": Normal, Metastatic and Non-metastatic
  • Default settings

Output: The definition of a right-skewed histogram of p-values, or "Conservative" p-values. I've been doing some research into how to interpret the results I got from DESeq2 and came across this:

My questions:

1) Are the p-values used for the histogram adjusted or are they the "raw" p-values?

2) Is there a flaw in my experimental design where I should be using 2 factors? (I've tried doing this intitally but after submitting, galaxy comes back with an error with 2 identical levels for the second factor)

Thanks, Reuben

rna-seq deseq2 • 210 views
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