Question: meta-analysis with RankProd
0
gravatar for Barbara Bo-Ju Shih
7.7 years ago by
Barbara Bo-Ju Shih40 wrote:
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]]
rankprod • 584 views
ADD COMMENTlink modified 7.7 years ago by Maciej Jończyk720 • written 7.7 years ago by Barbara Bo-Ju Shih40
Answer: meta-analysis with RankProd
0
gravatar for Maciej Jończyk
7.7 years ago by
Maciej Jończyk720 wrote:
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
ADD COMMENTlink written 7.7 years ago by Maciej Jończyk720
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 280 users visited in the last hour