Question: Right skewed histogram of p-values

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Giulio Di Giovanni •

**540**wrote:
Hi.
During a DE analysis, done with limma ebayes and toptable, the
histogram of the p-values doesn't show a high number of low p-values,
and not even an uniform distribution, which I may expect under the
null hypothesis of no-differentiation (right?), but something totally
skewed to the right: low freqencies for the small p-values and
increasing frequencies as the p-value on th x-axis increases.
here it is
http://img522.imageshack.us/img522/2169/testkpv.jpg
(I'm pretty sure about the correctness of the test. I did it on other
comparisons and it always gave nice and straightforward results).
I work on peptide arrays and I measure the immune-response.
Since the comparison I'm doing is between sick vs healthy individuals
for a pathology BUT all the individuals were also diagnosed as sick
for ANOTHER pathology, I explained the phenomenon with a confounding
effect of the second pathology, which is altering the immune-response,
and for which the data are not controlled.
But, from the data point of view, how can I comment on the graph? Does
anybody have an idea what we can say of a histogram of p-values where
we have few low p-values and many more high p-values?
Thanks in advance
G
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modified 8.9 years ago
by
Simon Anders •

**3.6k**• written 8.9 years ago by Giulio Di Giovanni •**540**