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Yanqin Yang wrote: > Hello, > > Does anyone know how to combine data sets derived from two different > affy mouse genome sets (U74 and MOE430_2) for data analysis? For > example, similar condition samples are hybridized with two types affy > chips. Is it possible to do normalization crossing different type > affy chips? Thanks! You would have to look it up, but I think the mouse4302 chip is based on newer annotation than the mgu74a. Anyway, there are only 43 overlapping probeset IDs (all AFFX-type control sequences), so there is no simple way to combine the two chip types. This technical issue aside, I don't think it would be a good idea anyway. I would have to imagine that the two chip types were run at very different times, and possibly by different people. This alone may introduce large batch effects that would make normalization together a Bad Idea. A better idea would be to normalize the data sets separately, and then use something like MergeMaid to find common genes between the two data sets, and then possibly something like GeneMeta to fit a mixed model. Best, Jim > > Yanqin > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Yanqin Yang wrote: > Hello, > > Does anyone know how to combine data sets derived from two different affy mouse > genome sets (U74 and MOE430_2) for data analysis? For example, similar condition samples are hybridized with two types affy chips. Is it possible to do normalization crossing different type affy chips? > Thanks! > > Yanqin > > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Look into the BMC Bioinformatics for the following article: CROPPER: A metagene creator resource for cross-platform and cross-species compendium studies. HTH, Andrej