Hi all, I am pretty new in this list so I hope my question is not going to be "inappropriate" for it ! Here is my problem: I have one human cell line Cw that is diploid and has a deficient gene FA, this cell line has been corrected for this deficient gene (name is Cneo), and I have also another cell line that evolved from Cw with 95% of cells being now tetraploid (and FA deficient, name Ctetra). I d like to compare this new tetraploid cell line to the 2 others. Besides, I have duplicates - and soon triplicates - for these in 2 different conditions applied to all these cells: normal culture conditions or incubation with a drug. I am using Affy HG U133A/B chips. I was wondering what kind of normalization I should use for a comparison such as Cw versus Ctetra without any drug ? Should I normalize all my diploid chips and then separately normalize all my tetraploid chips then pool them for analysis ? or can I normalize all the chips in the same process ? Then do my comparisons Thanks for your help Philippe Guardiola, MD [[alternate HTML version deleted]]

if i were analyzing this, my first attempt would be to use quantile normalization on all arrays at once. by default, you cant normalize 133A and 133B together so you would have to separate these. On Sat, 1 Mar 2003 Phguardiol@aol.com wrote: > Hi all, > I am pretty new in this list so I hope my question is not going to be > "inappropriate" for it ! Here is my problem: > I have one human cell line Cw that is diploid and has a deficient gene FA, > this cell line has been corrected for this deficient gene (name is Cneo), and > I have also another cell line that evolved from Cw with 95% of cells being > now tetraploid (and FA deficient, name Ctetra). I d like to compare this new > tetraploid cell line to the 2 others. Besides, I have duplicates - and soon > triplicates - for these in 2 different conditions applied to all these cells: > normal culture conditions or incubation with a drug. I am using Affy HG > U133A/B chips. I was wondering what kind of normalization I should use for a > comparison such as Cw versus Ctetra without any drug ? Should I normalize all > my diploid chips and then separately normalize all my tetraploid chips then > pool them for analysis ? or can I normalize all the chips in the same process > ? Then do my comparisons > Thanks for your help > Philippe Guardiola, MD > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >