Question: Is the bioconductor RRHO R package p-value computation for two.sided completely wrong ?
gravatar for Anthony
21 months ago by
Anthony0 wrote:

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) and log.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 that the former should be replaced by mean - count and (see EDIT below) the later should be divided by two. I am right?
  • 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,


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 .

ADD COMMENTlink modified 21 months ago • written 21 months ago by Anthony0
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: 2527 users visited in the last hour