Hi Jim (and others who replied off-list), Thank you -- when I saw the term "complete permutations", it didn't register in my head that it really meant combinations. Paul Quoting "James W. MacDonald" <jmacdon at="" med.umich.edu="">: > paul.boutros at utoronto.ca wrote: > > Hello, > > > > I'm having some troubles interpreting how/why siggenes performed a certain > > > number of permutations on my dataset. This is an affy dataset that was > > normalized by: > > > > data <- ReadAffy(filenames=cel.files, phenoData="phenodata.txt"); > > eset <- expresso(data, normalize.method="constant", > bgcorrect.method="none", > > pmcorrect.method="mas", summary.method="avgdiff"); > > > > I realize that the normalization is a bit unusual: this study is actually > > testing a range of normalization methods. This is a two-class experiment > with > > 3 arrays in each group: > > > > > >>eset; > > > > Expression Set (exprSet) with > > 22690 genes > > 6 samples > > phenoData object with 1 variables and 6 cases > > varLabels > > Group: read from file > > > >>design; > > > > [1] 1 1 0 1 0 0 > > > > > > So to do a SAM-like analysis I used: > > SAM.data <- sam(data=eset, cl=design, var.equal=FALSE, B=1000); > > > > And I expected there to be 6! = 720 total possible permutations. So I was > > > surprised to get this output: > > > >>SAM.data <- sam(data=eset, cl=design, var.equal=FALSE, B=1000); > > > > > > We're doing 20 complete permutations > > > > > > Why does siggenes think there are only 20 complete permutations to be used? > > > Have I done something wrong, or is my understanding of how the permutations > are > > done in error? > > It's a combination of incorrect terminology and (possibly) a > misunderstanding on your part. First, there *are* 720 possible > permutations, but we don't care about the ordering within each group > since we are simply comparing group means. What we really want here are > combinations, and there are only 20 combinations when you have 6 samples > and you are choosing three for each group (see ?choose). If you did all > 720 permutations it would result in only 20 unique t-statistics with a > lot of replication. > > This terminology is a hold over from SAM, which AFAIK really did do the > permutations rather than combinations. However, this is very wasteful of > computing time especially when the number of replicates gets large, so > siggenes rightly does the combinations and abuses terminology by calling > them 'complete permutations'. > > Best, > > Jim > > > > > > This is R 2.2.1 and siggenes 1.4.0 on WinXP. > > > > Paul > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald > University of Michigan > Affymetrix and cDNA Microarray Core > 1500 E Medical Center Drive > Ann Arbor MI 48109 > 734-647-5623 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues. >