Hi All, I have 5 CEL files from HGU133A and 5 from HGU133plus2. The first chip type has 22283 genes and the other has 54675 genes. I want to do RMA for all 10 files together taking only 22283 common genes from both chip types. How can I do it?? I would be thankful for your help. Regards, Abhishek Tripathi

Hi Abhishek, Abhishek Tripathi wrote: > Hi All, > > I have 5 CEL files from HGU133A and 5 from HGU133plus2. > The first chip type has 22283 genes and the other has > 54675 genes. > > I want to do RMA for all 10 files together taking only > 22283 common genes from both chip types. > > How can I do it?? I don't think you can. Well, not easily at least. The coordinates for the probes in a given probeset will be different for the two chips, so you won't be able to process them together using say, a modified cdf package and the rma() function. Theoretically, you could normalize and background correct the data, then extract the PM probe values for each probeset, put these data (on a probeset by probeset basis) in a matrix and run medianpolish(). However, this would be painfully time consuming. Not to mention any likely problems due batch effects. You would probably be better off processing each chip type separately and then trying to combine the data post-processing. And if you are trying to do a direct comparison of the 133a data to the plus2 data (e.g., detect differences between the 133a data and the plus2 data), then you might as well give up now, as any Biological differences will be aliased with batch/chip/time/processing differences. Best, Jim > > I would be thankful for your help. > > Regards, > Abhishek Tripathi > > _______________________________________________ > 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

Hi, I would recommend that you take a look at the MergeMaid package. http://astor.som.jhmi.edu/MergeMaid/mergemaid.pdf but there is also an older paper on it from Cope et al. http://www.bepress.com/sagmb/vol3/iss1/art29/ Best, David --- David Ruau Institute for Biomedical Engineering RWTH Aachen On Sep 19, 2007, at 11:12 AM, Abhishek Tripathi wrote: > > Hi All, > > I have 5 CEL files from HGU133A and 5 from HGU133plus2. > The first chip type has 22283 genes and the other has > 54675 genes. > > I want to do RMA for all 10 files together taking only > 22283 common genes from both chip types. > > How can I do it?? > > I would be thankful for your help. > > Regards, > Abhishek Tripathi > > _______________________________________________ > 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