How to correctly calculate Storey-Tibshriani FDR Q Values using R Package "QValue"?

Question

[Tom]

Hi all. I am trying to replicate the results of another paper.

The aim: I have a P value. Then I randomised the data set 1,000 times, and now I have another set of randomised P Values. As an example, let's say I have the p value below, and I've randomised the data set 10 times and I have 10 randomised p values:

Actual P Value = 0.03
Random P Values:

0.06
0.21
0.003
0.21
0.017
0.21
0.48
0.21
0.48
0.21

The exact technique that I want to do is: "Calculate the false discovery rate (FDR) (Q), defined as the number of expected false positives over the number of significant results (Storey and Tibshirani, 2003)".

I wrote this code using python, rpy2 and R:

import sys
import rpy2
import rpy2.robjects as ro
from rpy2.robjects import r
from rpy2.robjects.packages import importr

devtools = importr("devtools")
qvalue = importr("qvalue")

list1 = [float(line.strip()) for line in open(sys.argv[1])] #This is a list of 1,000 floats (randomised P Values)
pvals = ro.FloatVector(list1)
rcode = 'qobj <-qvalue(p=%s)' %(pvals.r_repr())
res = ro.r(rcode)
r_output1 = 'qobj$pvalue'
r_output2 = 'qobj$qvalue'
r_pvalue = ro.r(r_output1)
r_qvalue = ro.r(r_output2)
ListOfValues = zip(r_pvalue,r_qvalue)
for i in ListOfValues:
            print str(i[0]) + "\t" + str(i[1])

The output looks like this (a snapshot of my output for 1,000 p values):

P value Q value
0.21    0.032
0.48    0.04
0.21    0.032
0.81    0.068
0.017   0.017
0.48    0.047
0.81    0.06
0.017   0.017
0.211   0.03
0.81    0.068
0.069   0.023
0.069   0.023
0.069   0.023
0.48    0.047

I do not want an individual Q value for every randomised P value. I have an original P value (in this case 0.03), and I want one Q value to be associated with this P value; based on the set of randomised P Values. Could someone tell me where I've gone wrong in this code; or how I extract this information?

Thanks.

[SamGG]

Hi, I am not an expert, but I have the feeling that you mix fdr and bootstrap. May be those articles could help you with FDR. http://www.nature.com/nmeth/journal/v11/n4/full/nmeth.2900.html http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1135.html Best.