[BioC] quantile normalization

[H. Han]

Hi:

Does anyone has input on compatibility of "replicate-only" vs. "all-sample" quantile normalizations? I'd assume that "true significant" genes would be picked up by either "replicate-only" or "all-sample" method, though the latter is surely more conservative (by forcing the same distribution across all samples, replicates or not).  My analysis though seem to select two distinct lists of genes by two methods. e.g. If I pick top few hundreds from both lists, there'd be little overlap. Would it because my initial pool of genes are large (10,000 or so), or inherently these two methods are two assumptions, and not to be compared?

thanks in advance,

Hillary

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