I have two groups, C and A, where C is control. In both groups there are about 3,000 proteins. For each protein we acquire six measurements in both C and A (these are mass spectrometry intensities by the way). These measurements are paired.
I want to ask: "Are any of the proteins significantly different between C and A". I have performed 3,000 Wilcoxon paired tests and found some p-values < 0.05.
Is it correct to adjust for multiple hypotheses testing?
After I do correct all the p-values go to one, so nothing is significant. How should I interpret/present this?
Is it acceptable to rank the proteins according to the unadjusted p-values in order to determine which are most "interesting" and worth investigating further.