Entering edit mode
4.9 years ago
Anthony
•
0
Hi everybody,
I am trying to do some rank-rank hyper-geometric overlap with the RRHO R package. I am using alternative="two.sided".
The log p-value are very strange for multiple reasons (see R/ExpressionAnalysis.R
function numericListOverlap
):
- the 0 is not taken care of for the computation of the log. Does not -log(pval + eps) -- eps being a small number -- make a better choice?
- some p-values are above one.
2*the.mean - count
(see EDIT below) andlog.pval<- -log( phyper(q=lower+tol, m=a, n=n-a+1, k=b, lower.tail=TRUE) + phyper(q= upper-tol, m=a, n=n-a+1, k=b, lower.tail=FALSE))
are meaningless for me. I think thatthe former should be replaced by(see EDIT below) the later should be divided by two. I am right?mean - count
and - Additionally, I have absolutely no idea at all what the
tol
parameter means.
The package is downloaded more than 100 times by month and is the basis for RRHO2 publication. Consequently, I am puzzled to not find anything about those issues on the web.
Thanks in advance,
Anthony.
EDIT: The if-else construct with 2*the.mean - count
is equivalent to
absval <- abs(count - the.mean)
upper <- the.mean + absval ## same as `2*the.mean - count`
## for `count - the.mean < 0`
But I still do not understand, the p-values above one .