Hi Everyone,
I'm trying to determine the q values of my dataset using p-values generated by Fisher's tests from PLINK (allelic and genotypic). The p values are associated with SNPs relevant against clinical outcome. I am trying to determine the most significant SNPs from my analysis out of 70 SNPs.
After comparing both 'bootstrap' and 'smoother' qvalues output. I realize that some of the qvalues are < original p values after a certain threshold which is not the value reporting "qobj$pi0".
This output is definitely odd since I should expect qvalues to be > p values, especially when the pvalue is 1 and the qvalue (bootstrap) reported is 0.17286 (qobj$pi0 value)
If anyone can give me some clues, that would be great! I would be happy to paste my p-values if necessary.
Thanks in advance.
POST EDITED to include p-values (not sure how to attach a file here)
0.006211 0.231 0.1929 0.2727 0.0128 0.2003 0.02752 0.006144 1 0.6376 1 0.003863 0.002481 0.05531 0.02465 0.0141 0.0721 0.01738 0.0713 0.01848 0.02205 0.1721 0.03096 0.02307 0.06568 0.004345 0.0006609 0.00259 0.005319 0.0004572 0.0143 0.001896 0.02808 0.01518 0.1623 0.184 0.2339 0.2514 0.07164 0.04881 0.09818 0.1057 0.08894 0.07172 0.09818 0.1057 0.09542 0.1036 0.2362 0.2519 0.2516 0.2512 0.2186 0.1833 0.2036 0.1829 0.07978 0.04875 0.09542 0.1036 0.09361 0.1039 0.3349 0.3466 0.093 0.1488 0.042 0.02281 0.1044 0.07099 0.8093 0.8393 0.4839 0.441 0.8658 1 0.2296 0.2512 0.1019 0.1296 0.1154 0.1023 0.3635 0.1534 0.2095 0.2528 0.006035 0.001488 0.01061
Post the P values. Note that qvalue does not work as expected unless your P values have the correct distribution: uniform, with a possible (hopefully present) over-representation close to zero.