See below. On Tue, 2005-03-29 at 19:33 +0100, Mohammad Esad-Djou wrote: > Thanks for your help. > > > I have two other questions. > > 1. How can I compare an experiment correctly with a set of experiments in ma.plot? > > is this Ok? (for 7 Expriments) > > mat <- exprs( data.exprs ) > > ma.plot( mat[ , 1] + (mat[ , 2] + mat[ ,3] + mat[ ,4]+ mat[ ,5]+ mat[ ,6]+ mat[ ,7]), mat[ , 1] - (mat[ ,2] - mat[ ,3] - mat[ ,4] - mat[ ,5] - mat[ ,6] - mat[ ,7]) ) > Yikes ! What are you trying to do here ? Do you know about rowSums() and rowMeans(). The following is not what you have written above but what I think you want. rm27 <- rowMeans( mat[ , 2:7] ) ma.plot( mat[ ,1] - rm27, mat[ ,1] + rm27 ) I cannot comment on whether this is sensible because I never used ma.plot() on Affymetrix data. Perhaps other members of the mailing list might wish to comment on this. > 2. How can I save the result of ma.plot directly into a file (e.g. png or JPG...)? Two ways. a) With some forsight jpeg(file="lala.jpg") plot( 1:10 ) dev.off() b) or with hindsight plot(1:10) dev.copy2eps( file="lala.eps" ) > > Thanks, > Mohammad Esad-Djou > > > > > ramasamy@cancer.org.uk schrieb am 29.03.05 16:37:38: > > > > See comments below. > > > > On Tue, 2005-03-29 at 16:13 +0100, Mohammad Esad-Djou wrote: > > > Hello, > > > > > > I wrote a small program for MAS5.0: > > > > > > > > > library(affy) > > > library(affydata) > > > > > > data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL", > > > "./R/ME_cel/Expt2_R1.CEL") > > > > > > This is produce a syntax error. Try this > > > > ReadAffy( filenames=c("Expt1_R1.CEL", "Expt2_R1.CEL"), > > celfile.path="./R/ME_cel/") > > > > > > > > > data.exprs <- mas5(data.raw, sc=150) > > > rm(data.raw) > > > data.out <- cbind(483, "ME-mas5", "ME_Affy MAS5 Transformation (R)", data.exprs@exprs, 0) > > > write.table(data.out, file="./R/ME_data/aggregation_1.dat", sep="\t", col.names=NA, quote=FALSE) > > > rm(data.exprs, data.out) > > > > I find it easier to with the exprSet which can retrieved as > > > > mat <- exprs( data.exprs ) > > > > help.search("MA plot") suggests ma.plot in the affy package. You will > > have to decide what "M" and "A" means with affymetrix data. M could be > > difference in the two arrays and A could be the average > > > > ma.plot( mat[ , 1] + mat[ ,2], mat[ , 1] - mat[ ,2] ) > > > > > > > The result is written in aggregation_1.dat. Now, I would like to visualize result file with MAPlot, but I don't know, which intermediate steps are necessary. What can I do? > > > > > > Thanks, > > > Mohammad Esad-Djou > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > ______________________________________________________________ > Verschicken Sie romantische, coole und witzige Bilder per SMS! > Jetzt bei WEB.DE FreeMail: http://f.web.de/?mc=021193 > >