Hi Chintanu, Probably the reason it does not get a reply is because the issue has been discussed many times and searching the mailing list archive will allow you to read all of those discussions and decide what you want to do. My view is that you should not do it this way, but rather normalize similar things and then use appropriate statistical models to integrate the resulting data sets. But others have other opinions and there are many suggestions. Robert Chintanu wrote: > Hi All, > > I'm repeating my earlier post below, as it didn't bring any reply. > If you have worked in the mixture CDF environment, I would appreciate if you > could give me some direction, please. > > -------- > I'm trying to combine hgu133a and hgu133a2 for a single downstream analysis. > It is my first attempt, and have recently come across the idea of the > mixture CDF environment. As I try to move on down this road considering that > this is perhaps "the" option I have, eventually I could only sense that > something is going not in the right direction (as follows). > > Any suggestions and advice would indeed be valuable. > > Thanks. > > Chintanu > > > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] hgu133acdf_2.2.0 hgu133aprobe_2.2.0 hgu133a2probe_2.2.0 > hgu133a2cdf_2.2.0 matchprobes_1.12.0 MergeMaid_2.12.0 MASS_7.2-41 > [8] survival_2.34-1 affy_1.18.0 preprocessCore_1.2.0 > affyio_1.8.0 Biobase_2.0.0 > > >> cdfName(Data_A) # Data_A is ReadAffy () of a > set of CEL files > [1] "HG-U133A" > >> cdfName(Data_B) # Data_B is ReadAffy () of > another set of CEL files > [1] "HG-U133A_2" > > >> comBatch <- combineAffyBatch(list(Data_A, Data_B), c("hgu133aprobe", > "hgu133a2probe"), > newcdf = "hgu133aa2") > package:hgu133aprobe hgu133aprobe > package:hgu133a2probe hgu133a2probe > 241837 unique probes in common > >> Data_C=comBatch$dat >> hgu133aa2cdf=comBatch$cdf > >> "@"(Data_C, "cdfName", "hgu133aa2cdf") > [1] "hgu133aa2" >> "@"(Data_C, "cdfName") > [1] "hgu133aa2" > > >> class (Data_C) # Same for Data_A and Data_B > [1] "AffyBatch" > attr(,"package") > [1] "affy" > > > >> summary (Data_C) > Length Class Mode > 20 AffyBatch S4 > >> summary (Data_B) > Length Class Mode > 6 AffyBatch S4 > >> summary (Data_A) > Length Class Mode > 14 AffyBatch S4 > > >> show (Data_A) > AffyBatch object > size of arrays=712x712 features (8 kb) > cdf=HG-U133A (22283 affyids) > number of samples=14 > number of genes=22283 > annotation=hgu133a > notes= > >> show (Data_B) > AffyBatch object > size of arrays=732x732 features (8 kb) > cdf=HG-U133A_2 (22277 affyids) > number of samples=6 > number of genes=22277 > annotation=hgu133a2 > notes= > > >> show (Data_C) > AffyBatch object > size of arrays=0x0 features (8 kb) > cdf=hgu133aa2 (??? affyids) > number of samples=20 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain hgu133aa2 > Library - package hgu133aa2cdf not installed > Data for package affy did not contain hgu133aa2cdf > Bioconductor - hgu133aa2cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org