Something to be careful of -- I've worked around it, but don't have time for the real patch. The problem: split(exprSet,factor) fails, while split(exprSet,as.numeric(factor)) works: The example: R : Copyright 2002, The R Development Core Team Version 1.5.1 (2002-06-17) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type `license()' or `licence()' for distribution details. R is a collaborative project with many contributors. Type `contributors()' for more information. Type `demo()' for some demos, `help()' for on-line help, or `help.start()' for a HTML browser interface to help. Type `q()' to quit R. [Previously saved workspace restored] > options(STERM='iESS', editor='emacsclient') Warning message: using .GlobalEnv instead of package:annotate > library(Biobase) Loading required package: methods Expanding the signature to include omitted arguments in definition: j = "missing" Attaching package `Biobase': The following object(s) are masked from package:base : split > geary Expression Set (exprSet) with 4132 genes 8 samples phenoData object with 2 variables and 8 cases varLabels animal: Animal type: Specimen Type > split(geary,geary$animal) $"1" Expression Set (exprSet) with 4132 genes 2 samples phenoData object with 2 variables and 2 cases varLabels animal: Animal type: Specimen Type $"2" Expression Set (exprSet) with 4132 genes 2 samples phenoData object with 2 variables and 2 cases varLabels animal: Animal type: Specimen Type $"3" Expression Set (exprSet) with 4132 genes 2 samples phenoData object with 2 variables and 2 cases varLabels animal: Animal type: Specimen Type $"4" Expression Set (exprSet) with 4132 genes 2 samples phenoData object with 2 variables and 2 cases varLabels animal: Animal type: Specimen Type > geary$animal [1] 1 1 2 2 3 3 4 4 > split(geary,geary$type) $Gunk Expression Set (exprSet) with 2066 genes 8 samples phenoData object with 2 variables and 8 cases varLabels animal: Animal type: Specimen Type $Other Expression Set (exprSet) with 2066 genes 8 samples phenoData object with 2 variables and 8 cases varLabels animal: Animal type: Specimen Type > geary$type [1] Gunk Other Gunk Other Gunk Other Gunk Other Levels: Gunk Other > split(geary,as.numeric(geary$type)) $"1" Expression Set (exprSet) with 4132 genes 4 samples phenoData object with 2 variables and 4 cases varLabels animal: Animal type: Specimen Type $"2" Expression Set (exprSet) with 4132 genes 4 samples phenoData object with 2 variables and 4 cases varLabels animal: Animal type: Specimen Type > q() -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)