I am trying to analyze Affy microarray data. For this, I used limma package and I noticed that I get unexpected results aka none of the genes come out as significant. After checking the p value histograms, I noticed an unusual trend - histograms appeared to be hill shaped:
https://ibb.co/c15c5e I have done PCA and this has indicated two possible outliers but even if I remove them I still obtain the plot that is the same shape.
I assume this indicates that the wrong test was used. Does anyone know how I could possibly make the p plots appear to have a uniform distribution? Is there a different test that is used in this case?