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rdu234
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@rdu234-12828
Last seen 7.0 years ago
Hi
I have the RNA-seq data and I am comparing two groups of tissue (6 replicates each) to obtain the DE genes using DESeq2. When I plot the adjusted p-values as a histogram, I get a bimodal histogram with a right skew. The peak towards 1 disappears when I plot the p-values instead of adjusted p-values. Does this indicate a problem with read counts of any of the biological replicates?? Kindly help
Thanks for the reply. But could you please tell me why is the comparison giving me a bimodal curve? I have compared the same two groups with other tissue groups separately. I get a good histogram then with the adjusted p-values.
I don't know what you expect to see. Unlike plotting the p-values, what you are doing is not expected to be uniform (the null tests) plus a spike near 0 (the tests where null is rejectable).
I don't look at the histogram of adjusted p-values or have any ideas about interpreting this histogram.