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

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