Dear all, I am analysing HuGene2.0-st array affymetrix using aroma and limma package. I have 2 treatments and 3 arrays per condition. I have getting 11 genes that are differentially expressed, but these loose significance after applying fdr correction. I want to apply a filter out genes with similar distributions between treatments before applying fdr correction to see I am loosing significance due to overcorrection. Can someone advise me on a function or package to do this? I have explored genefilter and I could not find a function for this. Thanks for the help. Kind regards, Andreia ---------------------------------------------------------------------- ------------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]