Dear R members, I have this problem with 2 different Affy platforms. We started the experiment with U133A chips but had to switch in the middle to U133A_plus2. All the U133A are backordered with no delivery in sight. The two chips have the exact same gene probes and differ only in a few control probes. Naturally I will get an error in gcrma or ReadAffy but I was wondering if there is an easy way around this that will allow me to still normalize all my arrays together. Can I just ignore the control probes somehow? Maybe I need to modify the CDF file but I am not sure how complicated this is. Thanks, Yair

There are many posts dealing with this exact problem for these exact chips (for this exact reason I guess). Search the archives. Kasper On Feb 26, 2008, at 12:07 PM, Yair Benita wrote: > Dear R members, > I have this problem with 2 different Affy platforms. We started the > experiment with U133A chips but had to switch in the middle to > U133A_plus2. > All the U133A are backordered with no delivery in sight. The two > chips have > the exact same gene probes and differ only in a few control probes. > Naturally I will get an error in gcrma or ReadAffy but I was > wondering if > there is an easy way around this that will allow me to still > normalize all > my arrays together. Can I just ignore the control probes somehow? > Maybe I > need to modify the CDF file but I am not sure how complicated this is. > > Thanks, > Yair > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor