[BioC] log values of affybatch data

[Ben Bolstad]

On Tue, 2003-09-30 at 12:09, Ann Hess wrote:
> Does expresso ALWAYS return logged data?  For example, when calling the
> LiWong algorithm using


No expresso() does not always return log scale expression values.  In
fact I believe that only summary.method="medianpolish" returns log scale
expression values.  It should be pretty apparent by examining a few
expression values to confirm that this is the case. eg do something like

library(affy);library(affydata)
data(Dilution)
eset <-
expresso(Dilution,normalize.method="invariantset",bg.correct=FALSE,pmcorrect.method="pmonly",summary.method="liwong")

exprs(eset)[1:5,]


which, for me returns something like

               20A      20B      10A      10B
1000_at   639.2587 597.4893 665.5438 591.6256
1001_at   159.1597 149.6903 149.0489 152.0907
1002_f_at 337.3051 305.9068 312.6497 295.9938
1003_s_at 647.0458 626.9708 601.9409 592.7388
1004_at   353.2921 314.6988 318.9967 316.4813


which definitely look non-log scale to me