[BioC] Differences: mas5/mas5calls vs. call.expr/pairwise.comparison

[Benjamin Otto]

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
>
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