Hi, We are trying to compare affymetrix genelists generated a while back using MAS 5.0 to the new genelists generated using RMA analysis. Previously, we used to perform a comparison expression analysis of the replicates first (3 replicates for each condition) in order to determine the false positive rate. Is there a way to do something similar in RMA just for comparative purposes? Also, is it possible to compare only 2 chips at a time and generate a correlation coefficient? I checked the posting guide but couldn't find a previous email that would answer this question. Any help or pointing where to look is much appreciated, Thanks, Kai [[alternative HTML version deleted]]

Hi Kai, i'm not sure about your first question, but... re the correlation coefficient, take a look at the GeneSelector package. In their original paper, they called the correlation an OrderScore if I recall correctly. cheers, Mark ----------------------------------------------------- Mark Cowley, PhD Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- On 06/11/2009, at 5:37 AM, K Tre wrote: > Hi, > > We are trying to compare affymetrix genelists generated a while back > using MAS 5.0 to the new genelists generated using RMA analysis. > Previously, we used to perform a comparison expression analysis of the > replicates first (3 replicates for each condition) in order to > determine the > false positive rate. Is there a way to do something similar in RMA > just for > comparative purposes? > Also, is it possible to compare only 2 chips at a time and generate a > correlation coefficient? I checked the posting guide but couldn't > find a > previous email that would answer this question. > > Any help or pointing where to look is much appreciated, > Thanks, > Kai > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

Hi Kai, You can easily get correlation coefficients using R directly, but probably not AffylmGUI. >library(affy) >setwd("path_to_your_CELfiles") > rawdata <- ReadAffy() # this will read in all the CEL files in that directory # to get correlation coefficients on raw, PM probe-level data between all pairs of arrays: >cor(pm(rawdata)) >mas5data <- mas5(rawdata) >rmadata <- rma(rawdata) # to get correlation coefficients using mas5 values or rma values between all pairs of arrays: > cor(exprs(mas5data)) > cor(exprs(rmadata)) Don't forget that while the mas5 algorithm works independently on each array, the rma algorithm depends on which arrays are normalized together. HTH, Jenny At 11:45 AM 11/11/2009, K Tre wrote: >Hi Mark, > >Thanks for suggesting gene selector package, it might work. I am still >wondering whether it's possible to upload just 2 Affymetrix chips in >R/AffylmGUI and get a correlation coefficient rather than using Excel >or something else. Does anybody know? > >Thanks, >Kai > >On Thu, Nov 5, 2009 at 7:23 PM, Mark Cowley <m.cowley0 at="" gmail.com=""> wrote: > > > > Hi Kai, > > i'm not sure about your first question, but... > > re the correlation coefficient, take a look at the GeneSelector > package. In their original paper, they called the correlation an > OrderScore if I recall correctly. > > cheers, > > Mark > > ----------------------------------------------------- > > Mark Cowley, PhD > > > > Peter Wills Bioinformatics Centre > > Garvan Institute of Medical Research, Sydney, Australia > > ----------------------------------------------------- > > > > On 06/11/2009, at 5:37 AM, K Tre wrote: > > > >> Hi, > >> > >> We are trying to compare affymetrix genelists generated a while back > >> using MAS 5.0 to the new genelists generated using RMA analysis. > >> Previously, we used to perform a comparison expression analysis of the > >> replicates first (3 replicates for each condition) in order to > determine the > >> false positive rate. Is there a way to do something similar in > RMA just for > >> comparative purposes? > >> Also, is it possible to compare only 2 chips at a time and generate a > >> correlation coefficient? I checked the posting guide but couldn't find a > >> previous email that would answer this question. > >> > >> Any help or pointing where to look is much appreciated, > >> Thanks, > >> Kai > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> 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 > > > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu