[R] fdrtool qvalues

Hi, I've just started using R and fdrtool, and I'm not sure if the qvalues I'm receiving back are accurate. I performed fdrtool on pvalues obtained from a two way anova on proteomics data. So I have 266 data values (protein spots) for two factors (ft, vr, and the interaction) for each biologica

[R] fdrtool

Dear list members: I am using the package fdrtool to calculate qval from my input p values. My input pvalue ranged from 0.5-0. And the result I got for qval and lfdr are all much less than 0.01, I feel very confused about the result. The command used there is very easy: fdrtool(pvalue, statisti

[R] fdrtool help

Hello, I am using fdrtool(x, statistic="pvalue") where x is a vector of chisq p-values. I can get this command to work with some x, but not with others. When it does NOT work, I get the following screen output: > fdrtool(pvals$Chi2.pval, statistic="pvalue") Step 1... determine cutoff point Step 2.