I just started to work on low-level microarray data analysis and do not have experience in using RMA algorithm. I am now in a situation where I have to normalize a a few hundred of arrays across multiple tissues. I have seen a few messages regarding the legitimacy of using quantile-quantile (Q-Q) method to normalize many arrays across multiple tissue types in the bioconductor archive. It seems that normalization within tissue-of- origin was favored by some folks. Although I feel it is the approach I should take, I still hope to be more secure before I do it, just bacuse a lot of work will be done on the normalized data. Can anybody help by pointing out a few references that use Q-Q method within or not within tissue-of-origin? For those who has done Q-Q within the tissue-of-origin, could you please give some comments or your feelings regarding Q-Q withn tissue-of-origin? Hairong .

What do you mean by "normalization within tissue-of-origin" ? Can you give us examples of these messages/papers/references discussing this. I often work with finding differentially expressed genes between two phenotypes of the same type of cancer and tissue type. How would this normalisation work then ? Regards, Adai On Thu, 2004-09-09 at 16:43, Hairong Wei wrote: > I just started to work on low-level microarray data analysis and do not have > experience in using RMA algorithm. I am now in a situation where I have to > normalize a a few hundred of arrays across multiple tissues. I have seen a > few messages regarding the legitimacy of using quantile-quantile (Q-Q) > method to normalize many arrays across multiple tissue types in the > bioconductor archive. It seems that normalization within tissue- of-origin > was favored by some folks. Although I feel it is the approach I should > take, I still hope to be more secure before I do it, just bacuse a lot of > work will be done on the normalized data. > > Can anybody help by pointing out a few references that use Q-Q method within > or not within tissue-of-origin? For those who has done Q-Q within the > tissue-of-origin, could you please give some comments or your feelings > regarding Q-Q withn tissue-of-origin? > > Hairong > > . > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >