Hi, I am trying to carry out meta-analysis on 4 sets of gene expression microarray data using RankProd. I'm having the following problems: - 3 of the data sets are one channel (with normalised intensity) and one is two channel (common reference) with log 2 ratio of the two channels. Can I just log2-transform the normalised intensity in the one channel data sets and compare them like that? - In addition, 2 studies contain internal control, 1 study contain external controls only, and 1 study contain both internal and external controls. Is it possible to use paired test in RankProd? Would it be inaccurate if I do not use paired test? Thank you for your help Barbara [[alternative HTML version deleted]]

Hi Barbara, > Can I just log2-transform the normalised intensity in the one channel > data sets and compare them like that? I advise you to transform your log2 data to probability of expression scale (POE, available in metaArray and poe packages). see paper Ramasamy A, Mondry A, Holmes CC, Altman DG (2008) Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 5(9): e184. doi:10.1371/journal.pmed.0050184. I've found it useful. Best Wishes, Maciej -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com