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This might be slightly faster apply( Exprs, 1, function(x){ anova( lm( x ~ scheme ) )[1,5] } ) and should get you the correct names from Exprs. BTW, have you considered using LIMMA which is designed for such purposes. Regards, Adai On Mon, 2005-07-11 at 12:19 +0200, Marcin Piechota wrote: > Hi > > I have problem with very long lasting time of anova in R. > > My script: > Exprs <- exprs(eset) > Anno <- geneNames(eset) > scheme <- gl(4,3,12, labels=c("a", "b","c", "d")) > x<-matrix(1:90202,nrow=45101, ncol=2) > for (i in 1:45101) { > Data = Exprs[i,] > results <- lm(Data~schemat) > nextstep <- anova(results) > x[i,] <- c(Anno[i],nextstep[1,5]) > } > > where "eset' is rma normalized affy data from m430v2 > > this script lasts for about 20 minutes > on P4 3GHz, 4GB RAM > > How to make it shorter? > > Marcin Piechota > Institute of Pharmacology PAS Krakow > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Marcin, the only dramatic speedup I can think about is to use limma instead of R's lm. Otherwise 20 min for 45k anovas in R is not too bad, isn't it? kind regards, Arne -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Marcin Piechota Sent: Monday, July 11, 2005 12:19 To: bioconductor at stat.math.ethz.ch Subject: [BioC] CPU time of Anova in R Hi I have problem with very long lasting time of anova in R. My script: Exprs <- exprs(eset) Anno <- geneNames(eset) scheme <- gl(4,3,12, labels=c("a", "b","c", "d")) x<-matrix(1:90202,nrow=45101, ncol=2) for (i in 1:45101) { Data = Exprs[i,] results <- lm(Data~schemat) nextstep <- anova(results) x[i,] <- c(Anno[i],nextstep[1,5]) } where "eset' is rma normalized affy data from m430v2 this script lasts for about 20 minutes on P4 3GHz, 4GB RAM How to make it shorter? Marcin Piechota Institute of Pharmacology PAS Krakow [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor