[BioC] Question on normalization

[Gordon Barr]

To Bioconductor

We have used the quantile normalization method in Bioconductor and would
like to know if there is consensus (or if not what are the opinions) about
whether or not to normalize all experimental conditions and controls
together or to analyze each group separately. We have two experimental
groups and one control with multiple replicates for each from different
animals.  The three conditions were run at the same time for each replicate
to minimize variability between groups. It seems to us that if we normalize
both experimental groups and controls together we will bias the results
against ourselves, even if most gene expression levels are unchanged.

Thanks


Gordon 



Gordon A. Barr, Ph.D.
Professor Of Psychology
Hunter College, CUNY
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Senior Research Scientist
Developmental Psychobiology
NYS Psychiatric Institute
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