Dear Bioconductor users, I want to analyze a set of spotted arrays with an irregular spotting design, so “avereps” seems to be appropriate to get averaged expression values for each transcript. However, applying this to my data > dim(my.arrays) [1] 11520 18 > is(my.arrays) [1] "MAList" "list" "LargeDataObject" "vector" produces the following error: > averaged<-avereps(my.arrays) Error in avereps.default(x$M, ID = ID) : (subscript) logical subscript too long Can anyone give me a hint what’s going wrong here? Thanks a lot in advance, Claus-Jürgen Scholz > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=Germ an_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.8.0 affy_1.20.0 Biobase_2.2.0 lattice_0.17-15 limma_2.16.0 loaded via a namespace (and not attached): [1] affyio_1.10.0 grid_2.8.0 preprocessCore_1.4.0 [[alternative HTML version deleted]]