Dear BioC people Crispin Miller was so kind to inform me that this bug has been solved in version 2.10, as you can see from the following R session: # Package "simpleaffy" version 2.10: correct present calls > data <- ReadAffy() > pval <- detection.p.val(data) Getting probe level data... Computing p-values Doing PMA Calls > pval.c <- pval$call > pval.p <- pval$pval > pval.pc <- cbind(pval.p,pval.c) > pval.ord <- pval.pc[order(as.double(pval.pc[,1])),] > pval.ord[1:4,] V0632.CEL.detection.p.val V0632.CEL.present AFFX-hum_alu_at "0" "P" AFFX-BioB-M_at "4.430552596021e-05" "P" AFFX-BioC-3_at "4.430552596021e-05" "P" AFFX-BioDn-5_at "4.430552596021e-05" "P" > Best regards Christian Stratowa > -----Original Message----- > From: Stratowa,Dr.,Christian FEX BIG-AT-V > Sent: Monday, March 14, 2005 12:49 > To: 'bioconductor@stat.math.ethz.ch' > Cc: 'cmiller@picr.man.ac.uk' > Subject: [BioC] simpleaffy function detection.p.value - bug > > Dear BioC people > > Sorrowly, until now I did not receive any reply to my former message. > Meanwhile I have compared the output from detection.p.val (simpleaffy) > with the output from mas5calls (affy). > As shown in the two R sessions below, the output from detection.p.val has > the described bug, while the > output from mas5calls is correct. > > # Package "simpleaffy" version 2.01: Bug in present call > > data <- ReadAffy() > > pval <- detection.p.val(data) > Getting probe level data... > Computing p-values > Doing PMA Calls > > pval.c <- pval$call > > pval.p <- pval$pval > > pval.pc <- cbind(pval.p,pval.c) > > pval.ord <- pval.pc[order(as.double(pval.pc[,1])),] > > pval.ord[1:4,] > V0632.CEL.detection.p.val V0632.CEL.present > AFFX-hum_alu_at "0" "P" > AFFX-BioB-M_at "4.430552596021e-05" "A" > AFFX-BioC-3_at "4.430552596021e-05" "A" > AFFX-BioDn-5_at "4.430552596021e-05" "A" > > > > # Package "affy" version 1.5.8: correct present calls > > data <- ReadAffy() > > pres <- mas5calls(data) > Getting probe level data... > Computing p-values > Making P/M/A Calls > > pres.c <- exprs(pres) > > pres.p <- se.exprs(pres) > > pres.pc <- cbind(pres.p,pres.c) > > pres.ord <- pres.pc[order(as.double(pres.pc[,1])),] > > pres.ord[1:4,] > V0632.CEL V0632.CEL > AFFX-hum_alu_at "0" "P" > AFFX-BioB-M_at "4.40550144861514e-05" "P" > AFFX-BioC-3_at "4.40550144861514e-05" "P" > AFFX-BioDn-5_at "4.40550144861514e-05" "P" > > > > It would be great if this bug could be corrected in a newer version of > simpleaffy. > > Best regards > Christian Stratowa > > > > >