I would like to know what the best solution is in analyzing data from the same yource hybridized to hgu133a and hgu133b chips. 1. Shall the arrays be normalized sperately and merged afterwards? But then the question arises how to annotate, because there is no such environment available 2. Shall the arrays be merged into one affyBatch before normalization? How can I do smth like this. Which packages have the appropriate functions? 3. What about the similar sequences? Is there smth to worry about? 4. Is this not a problem often encounterd by analysits? Is there such a function which merges the two environments automatically? Thanks a lot for your help Michael

I asked this question before and used almost the same subject line as you did (mine was "Combining HGU133A & HGU133B data"). See http://files.protsuggest.org/biocond/html/3268.html IMHO, it is better to do 1). But if you insist on 2), this may be possible using the suggestion in Laurent Gautier's reply but I think there might new functions since the posting that could do this. As Crispin Miller suggested, you have 2000+ probesets that you can to use as quality check or calibrate. On Thu, 2004-11-11 at 17:09, Auer Michael wrote: > I would like to know what the best solution is in analyzing data from the > same yource hybridized to hgu133a and hgu133b chips. > 1. Shall the arrays be normalized sperately and merged afterwards? > But then the question arises how to annotate, because there is no such > environment available > 2. Shall the arrays be merged into one affyBatch before normalization? How > can I do smth like this. Which packages have the appropriate functions? > 3. What about the similar sequences? Is there smth to worry about? > 4. Is this not a problem often encounterd by analysits? Is there such a > function which merges the two environments automatically? > > Thanks a lot for your help > > Michael > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Adaikalavan Ramasamy ramasamy@cancer.org.uk Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Cancer Research UK Tel : 01865 226 677 Old Road Campus, Headington, Oxford Fax : 01865 226 962