Hi I´ve done an array experiment using Affymetrix arrays and I was quite happy with the analysis (GCRMA) till the other day. A guy in a meeting told me that Affy chips have all these controls which I thought were great, but he insisted that the mismatch-probes are more a pain than a good idea. He suggested I should re-analyse the arrays without the mismatched- results. Here is the question, what do you think? and if you agree, does any of you know an script to get rid of them? (I can use R, but very bluntly) Cheers marta Marta Agudo PhD Departamento de Oftalmología Facultad de Medicina Campus Espinardo 30100 Murcia- Spain Phone:+34 968363996 [[alternative HTML version deleted]]

Marta Agudo wrote: > Hi > I?ve done an array experiment using Affymetrix arrays and I was quite happy > with the analysis (GCRMA) till the other day. A guy in a meeting told me > that Affy chips have all these controls which I thought were great, but he > insisted that the mismatch-probes are more a pain than a good idea. He > suggested I should re-analyse the arrays without the mismatched- results. > Here is the question, what do you think? and if you agree, does any of you > know an script to get rid of them? (I can use R, but very bluntly) If you use rma() in the affy package, you will be doing essentially the same thing as gcrma() but without the step that uses the MM probes to estimate background. Also note that gcrma() doesn't use the MM probes in a naive way like Affy's MAS4 or MAS5, but estimates the true background after accounting for the 'stickiness' of the probe, based on the GC content. Best, Jim > > Cheers > marta > > > Marta Agudo PhD > Departamento de Oftalmolog?a > Facultad de Medicina > Campus Espinardo > 30100 Murcia- Spain > Phone:+34 968363996 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623