Question: Highly biased experiment showing funny histogram of p values for all tests. Suggestions?
gravatar for Mozart
10 months ago by
Mozart190 wrote:

Dear all, I am struggling (as usual) with a really important/expensive experiment we manage to complete. Having done this in different days, plus given the fact we are not expecting a strong phenotype (we are treating cells with a molecule that shouldn't change these ones that much), I would imagine not so many genes differentially expressed. Perfect. I initially corrected the experiment for batch effect. If I plot the histogram of p values I get something like this: enter image description here Which is pretty odd I guess, given the fact I get a lot of unfiltered values in my final experiment that are around pval=1.

then, I decided to remove low counts and then,

dds$condition <- relevel(dds$condition, ref = "B")
dds <- DESeq(dds)

results_A_vs_B<-results(dds, c("condition", "A", "B"))

it's even worse, I guess:

enter image description here

So there's no doubt there's something wrong here but not sure how to get rid of it.

Do you have any ideas?


filtering rna-seq deseq2 • 331 views
ADD COMMENTlink modified 20 days ago • written 10 months ago by Mozart190

I cannot see the figures, is it me or something went wrong?

ADD REPLYlink written 10 months ago by Fabio Marroni2.5k

How to add images, biostar post: How to add images to a Biostars post

ADD REPLYlink written 20 days ago by lieven.sterck7.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 647 users visited in the last hour