Would anyone have experience or opinions about comparing hgu133a chips with a starting amount of 3mg total RNA to some chips with a starting amount of 1mg total RNA? I have a 12 chip experiment, but two of the chips have the lower starting total RNA. Visually, the two lower RNA chips are quite distinctive in comparing boxplots for the raw data, but the gcrma results look quite comparable. This brings up a more general question of how much can the starting total RNA for these types of arrays vary and still be compared using gcrma? Thanks for any ideas or suggestions, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099

one would hope that bolstad's quantile normalization would make them comparable. gcrma uses this normalization by default. but in my opinion one can only answer this question with data. On Mon, 29 Sep 2003, Dick Beyer wrote: > Would anyone have experience or opinions about comparing hgu133a chips with a starting amount of 3mg total RNA to some chips with a starting amount of 1mg total RNA? I have a 12 chip experiment, but two of the chips have the lower starting total RNA. > > Visually, the two lower RNA chips are quite distinctive in comparing boxplots for the raw data, but the gcrma results look quite comparable. > > This brings up a more general question of how much can the starting total RNA for these types of arrays vary and still be compared using gcrma? > > Thanks for any ideas or suggestions, > Dick > ******************************************************************** *********** > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >