Genomic screen- Benjamini–Hochberg procedure

#1
Hi,

It is the first time I try to use forum
,
I am not sure if it is the correct place to ask but.......

I have NGS data of 12,500 unique sgRNA. I wanted to compare the abundance, of every sgRNA, between four control samples to four treatment samples.
For doing so I have used R and got the p-value by doing multiple comparison t-test.
I have received 12,500 p-values.


The command - p.adjust(p,method="BH") to was used to calculate the corrected p-value.

Now for my question:
Seven sgRNA's, out of the pool of 12,500, are predicted to be enriched in my treatment sample.


If I assume these seven sgRNA's would be enriched, based on previews published studies, is it correct to rank the p-value of the seven sgRNA's higher in my BH analysis for corrected p-value?

Here is the code I would use:

ordered.p <- sort(p)
critical.vals <- NULL
bh.fdr.adjusted.p <- NULL
for (i in 1:length(ordered.p)) {
temp <- (i/length(ordered.p))*0.05
critical.vals <- c(critical.vals,temp)
bh.fdr.adjusted.p <- c(bh.fdr.adjusted.p, min((ordered.p*length(ordered.p)/i),1))


}

final.out <- cbind(ordered.p,critical.vals,bh.fdr.adjusted.p)

 

Dason

Ambassador to the humans
#2
I don't quite get what you're doing. What are you trying to get that p.adjust doesn't already provide?