I'm getting a strange error (see below). I also tried the Harvard bpmaps for NCBIv36, but they give a different error. Code: library(pdInfoBuilder) # symbolically linked from ~/LabNotebook/, actually in /work/jwoods/ subdirs on Einstein. # bpmapFile <- "Hs35b_P01R_v01-3_NCBIv36.NR.bpmap" # Harvard version # Harvard version appears to not work with the Affy cif. Need a different cif from # somewhere. bpmapFile <- "Hs35b_P01R_v01-3_NCBIv34.bpmap" # Affy version cifFile <- "Hs35b_P01R_v01.cif" obj <- new("AffyTilingPDInfoPkgSeed", version="0.0.1", author="John O. Woods", email="john.woods at mail.utexas.edu", biocViews="AnnotationData", genomebuild="NCBI Build 34", bpmapFile=bpmapFile, cifFile=cifFile) makePdInfoPackage(obj, destDir="/work/jwoods/pd-packages") Error message for Affy bpmaps: Creating package in /work/jwoods/pd- packages/pd.hs35b.p01r.v01.3.ncbiv34 Error in rbind(cbind(do.call(cbind, u[cols.pm]), atom = 1:length(u[[2]]), : number of columns of matrices must match (see arg 2) Timing stopped at: 22.73 0.576 23.331 > Alternatively, the error message for the Harvard bpmaps: Creating package in /work/jwoods/pd.hs35b.p01r.v01.3.ncbiv36.nr Error in sqliteExecStatement(conn, statement, bind.data, ...) : RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be unique) Timing stopped at: 14.441 0.14 14.577 This is all for the Affy human tiling array. Thoughts? Thanks, John