Newbie. quantile normalization should be done on all conditions or within replicates of each condition?
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@ali-mohammadian-5008
Last seen 9.6 years ago
Hi all! Newbie here. I wondered wh ether quantile normalization should be done on an array containing all conditions of 1 experiment (eg containing both patients and healthy people) or within replicates of each condition (eg on data from patients and on data from healthy people separately)? Thanks indeed.
Normalization Normalization • 595 views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
You should normalize all conditions together, unless you have reason to suspect that the assumptions for a quantile normalization (most genes are not differentially expressed) does not hold. Best, Jim On 5/30/2012 5:38 AM, Cytochalasin wrote: > Hi all! > > Newbie here. > > I wondered wh ether quantile normalization should be done on an array > containing all conditions of 1 experiment (eg containing both patients > and healthy people) or within replicates of each condition (eg on data > from patients and on data from healthy people separately)? > > Thanks indeed. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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