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