Dear all, I have been using GCRMA for the last month or so, jumping from AFFY MAS5 since everybody agreed GCRMA is better. Now I am having some doubts about the way to use it. It was not clear to me from the beginning if I could normalize all the data from different treatments at once or that I would have to treat separately the repeats. MAS5 is one chip at a time (no linear model). How do you use GCRMA? In my case I have 7/7/2 repeats for 3 different "treatments" (cell populations sorted in different ways). How should I proceed? Also what if I don't have any repeats and only one chip for each "treatment"?. Until now I have loaded all A chips and GCRMA all of them together. Thanks for helping, Radu -- Dr. Radu Dobrin Department of Molecular Biology Princeton University Washington Road Princeton, NJ 08544-1014 Phone: 609-258-5657 E-mail: rdobrin@molbio.princeton.edu

Hello, If you are interested in investigating the 3 different cell sorting methods and you use ANOVA for downstream analysis you have to normalize the data together, otherwise you won't be able to distinguish between the real treatment effect and "random" fluctuations. kind regards, Arne > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of > Radu Dobrin > Sent: 27 January 2005 15:47 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] GCRMA question > > > Dear all, > > I have been using GCRMA for the last month or so, jumping > from AFFY MAS5 > since everybody agreed GCRMA is better. Now I am having some doubts > about the way to use it. It was not clear to me from the > beginning if I > could normalize all the data from different treatments at > once or that I > would have to treat separately the repeats. MAS5 is one chip > at a time > (no linear model). How do you use GCRMA? In my case I have > 7/7/2 repeats > for 3 different "treatments" (cell populations sorted in different > ways). How should I proceed? Also what if I don't have any > repeats and > only one chip for each "treatment"?. > > Until now I have loaded all A chips and GCRMA all of them together. > > Thanks for helping, > Radu > > -- > Dr. Radu Dobrin > Department of Molecular Biology > Princeton University > Washington Road > Princeton, NJ 08544-1014 > Phone: 609-258-5657 > E-mail: rdobrin@molbio.princeton.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >