Hello, I am attempting to modify TPMAP files and then back-convert them to BPMAP files using the writeTpmap {affxparser} command. To start, I attempted to convert BPMAP to TPMAP and back to BPMAP using an Affymetrix BPMAP file which I know can work with my CEL files. But when I try to use the back-converted file to process my tiling array CEL files, I get this error: [1] "WARNING: The input CEL file suggests a different platform than the PBMAP file." [1] "CEL platform: 'At35b_MR_v04'" [1] "BPMAP filename: 'tmp.bpmap'" Error in AnalyzeTilingCelFiles(CEL.NAMES, bf, outfilename = "btmp.tsv", : ERROR!! Wrong BPMAP file?! Exiting! It appears that a BPMAP file created via writeTpmap and tpmap2bpmap is incompatible with the AnalyzeTilingCelFiles function. What am I doing wrong? Here is the code I am trying to run: library(Biobase) library(affy) library(preprocessCore) library(affxparser) library(AffyTiling) # original obsolete BPMAP from Affymetrix of = 'At35b_MR_v04-2_TIGRv5.bpmap' # TPMAP tf = 'tmp.tpmap' # BPMAP bf = 'tmp.bpmap' bpmap = readBpmap(of) # write it in text format writeTpmap(tf,bpmap,verbose=1) # convert it back to BPMAP tpmap2bpmap(tf,bf,verbose=1) # these are from GSE9646 CEL.NAMES = c("GSM243682.CEL", "GSM243683.CEL", "GSM243684.CEL", "GSM243685.CEL") # the original works fine AnalyzeTilingCelFiles(CEL.NAMES,of,outfilename="otmp.tsv",readOnlyNCBI =FALSE) # now try to use the new one AnalyzeTilingCelFiles(CEL.NAMES,bf,outfilename="btmp.tsv",readOnlyNCBI =FALSE) Sincerely, Ann Loraine [[alternative HTML version deleted]]