gistfile1.r

arrayQualityMetrics(expressionset=msc.data,
                    outdir='report_raw',
                    force=TRUE,
                    do.logtransform=TRUE)

# Normalize and create second report
msc.eset <- call.exprs(msc.data, "rma");
arrayQualityMetrics(expressionset=msc.eset,
                    outdir='report_rma',
                    force=TRUE,
                    do.logtransform=FALSE)