Question: DESeq2 p-value histogram
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reuben.schndr123 • 0 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: http://varianceexplained.org/statistics/interpreting-pvalue-histogram/
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