Dear all, I am using the oligo package to analyse affymetrix tiling array data and I don't understand why PM and MM do not have the same length... Here is the code: > #### READ CEL FILES > TOTAL_DATA = read.celfiles(exp_file,pk="tilingcdf") Incompatible phenoData object. Created a new one. Platform design info loaded. > x=pmindex(TOTAL_DATA) > length(x) [1] 3092374 > y=mmindex(TOTAL_DATA) > length(y) [1] 3092338 > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: tilingcdf oligo BufferedMatrixMethods "1.0.0" "1.0.2-6" "1.0.0" BufferedMatrix RSQLite DBI "1.0.1" "0.5-6" "0.2-3" affyio Biobase "1.4.1" "1.14.0" Thanks, Naira -- ================================================================== Naira Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.ugent.be http://www.psb.ugent.be