All- I have been attempting to compare sequences on the HGU133 Plus 2.0 chip to the HT HGU 133+ PM. I am doing this to compare values of vectors in frma. The HT chip is a subset of HGU133 Plus 2.0 with mismatch probes removes and some probesets reduced in size. Looking at the probe package: hthgu133pluspmprobe$sequence: 519370 However, when looking at an Affybatch object made from HT CEL files: Taking an Affybatch object: 'dat' Index <- pmindex(dat) tv = unlist(Index) length(tv) #536460 It appears that the Affybatch reports that there are 536460 sequences and the hthgu133pluspmprobe package is reporting only 519370. What is the difference? It is possible to find the information on the 17090 sequences not in the hthgu133pluspmprobe package? Thanks for any information or direction. Eric Zollars Session info below: bioconductor 2.13, R 3.0.2 > sessionInfo() R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.40.0 hthgu133pluspmcdf_2.13.0 hgu133plus2frmavecs_1.3.0 [4] hgu133plus2probe_2.13.0 hthgu133pluspmprobe_2.13.0 AnnotationDbi_1.24.0 [7] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 DBI_0.2-7 IRanges_1.20.6 [4] preprocessCore_1.24.0 RSQLite_0.11.4 stats4_3.0.2 [7] tools_3.0.2 zlibbioc_1.8.0 [[alternative HTML version deleted]]