Hi, I have done some experiments using amplified RNA (Rayan Baugh's method which I modified slightly) probes with affy chips. The study design is a simple comparison of knockout mutant vs wild type. My question was: Is it ok to use the same statistical algorithms one would apply for standard microarray experiments or do I need to follow a different strategy? Can anybody give pointers? Thanks, Swati Swati Ranade Bauer Center for Genomics Research 7 Divinity Av Cambridge MA 02138

One of the problems with amplified mRNA is that not all mRNA species are going to get amplified at the same rate (and probably for some the rate is zero), also, as I understand it the resulting mRNAs will tend not to be full length. So this affects the binding, and hence the estimated expression levels (and I do not believe it matters what platform you are using; there will most likely be some peculiarities). So, that basically means that you want all samples to have been amplified using the same method, and in some sense the same amount. Otherwise, you are not really comparing like with like. The RNA degredation plots can be quite helpful in this regard - as they can help to pinpoint arrays that might be substantially different. Robert On Feb 9, 2005, at 5:36 AM, Swati Ranade wrote: > Hi, > I have done some experiments using amplified RNA (Rayan Baugh's method > which > I modified slightly) probes with affy chips. The study design is a > simple > comparison of knockout mutant vs wild type. My question was: Is it ok > to use > the same statistical algorithms one would apply for standard microarray > experiments or do I need to follow a different strategy? Can anybody > give > pointers? > > Thanks, > > Swati > > Swati Ranade > Bauer Center for Genomics Research > 7 Divinity Av > Cambridge > MA 02138 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+