Dear BioC members, in my last calculations I noticed that the affy-package combination of mas5() and mas5calls() results in different Present/Absent calls than the simpleaffy-package version with call.exprs() and pairwise.comparison(). That was the more surprising for me as I thought simpleaffy was just some wrapper around the affy-package automating some high-level steps. A comparison of the results with the ones returned by the affymetrix software revealed that the simpleaffy version is nearly identical while the affy version is different one. Is there some error in my code? The exact commands I used were: x <- read.affy() #version 1: mas <- mas5(x,sc=sometgt) mas.call <- mas5calls(x) #version 2: simplemas <- call.exprs(x,"mas5",sc=sometgt) simplemas.cmp <- pairwise.comparison(simplemas,"treatment",spots=x) regards Benjamin

I just checked the expresson values returned by the two methods. The interesting thing is, mas5(x,sc=sometgt) yields results nearly identical to the affymetrix ones. The simplaffy call.exprs(x,"mas5",sc=sometgt) return values a little bit different different. Looking the resulting values it makes no big difference if I call call.exprs() with "mas5" or "mas5-R". So why do I get such different results? Here are my first five rows: > smp2 <- call.exprs(x,"mas5-R",sc=sometgt) > exprs(smp2)[1:5,] 1026_HG-U133.CEL 62_HG-U133.CEL 1007_s_at 4.850861 4.657905 1053_at 2.438049 3.517322 117_at 4.199809 4.803548 121_at 6.758776 6.241071 1255_g_at 4.450771 1.855238 > exprs(simplemas)[1:5,] 1026_HG-U133.CEL 62_HG-U133.CEL 1007_s_at 4.851125 4.658149 1053_at 2.438313 3.517566 117_at 4.200072 4.803792 121_at 6.759039 6.241314 1255_g_at 4.451034 1.855482 > exprs(mas)[1:5,] 1026_HG-U133.CEL 62_HG-U133.CEL 1007_s_at 28.857236 25.244638 1053_at 5.419085 11.450371 117_at 18.376736 27.926217 121_at 108.291468 75.639653 1255_g_at 21.868322 3.618115 > log(exprs(mas))[1:5,] 1026_HG-U133.CEL 62_HG-U133.CEL 1007_s_at 3.362361 3.228614 1053_at 1.689927 2.438022 117_at 2.911086 3.329566 121_at 4.684826 4.325981 1255_g_at 3.085039 1.285953 and here is a copy of the corresponding function calls of mas5() and call.exprs(): > mas5 function (object, normalize = TRUE, sc = 500, analysis = "absolute", ...) { res <- expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas", normalize = FALSE, summary.method = "mas", ...) if (normalize) res <- affy.scalevalue.exprSet(res, sc = sc, analysis = analysis) return(res) } #calls.exprs ... else if (algorithm == "mas5-R") { if is.na(method)) { tmp1 <- expresso(x, normalize = FALSE, bgcorrect.method = "mas", pmcorrect.method = "mas", summary.method = "mas") tmp <- affy.scalevalue.exprSet(tmp1, sc = sc) } else { tmp1 <- expresso(x, normalize.method = method, bgcorrect.method = "mas", pmcorrect.method = "mas", summary.method = "mas") tmp <- affy.scalevalue.exprSet(tmp1, sc = sc) } ... else if (algorithm == "mas5") { tmp <- justMAS(x, tgt = sc) if (!do.log) { exprs(tmp) <- 2^exprs(tmp) } ... I don't really see the difference. regards, benjamin > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Benjamin > Otto > Sent: 16 February 2006 10:25 > To: BioClist > Subject: [BioC] Differences: mas5/mas5calls vs. > call.expr/pairwise.comparison > > > Dear BioC members, > > in my last calculations I noticed that the affy-package combination of > mas5() and mas5calls() results in different Present/Absent calls than the > simpleaffy-package version with call.exprs() and > pairwise.comparison(). That > was the more surprising for me as I thought simpleaffy was just > some wrapper > around the affy-package automating some high-level steps. A comparison of > the results with the ones returned by the affymetrix software > revealed that > the simpleaffy version is nearly identical while the affy version is > different one. Is there some error in my code? > The exact commands I used were: > > x <- read.affy() > > #version 1: > mas <- mas5(x,sc=sometgt) > mas.call <- mas5calls(x) > > #version 2: > simplemas <- call.exprs(x,"mas5",sc=sometgt) > simplemas.cmp <- pairwise.comparison(simplemas,"treatment",spots=x) > > > regards > Benjamin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >