Hi Ben, there seem to be two bugs in the C code for read.affybatch in the package affy, i.e. in read_abatch.c. On my installation (R 1.9 devel on linux), they lead to "SIGSEGV, Segmentation fault" 1. In the function "isgzTextCelFile", the file is opened via "gzopen", but closed via "fclose" (I think it should be "gzclose"). 2. The function sometimes exits without closing, through the line if (strncmp("[CEL]", buffer, 4) != 0) return 0; The same applies to "isTextCelFile". Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber

... for anyone who cares about reading gzipped CEL files in the old text format with read.affybatch: that has been fixed and should be available from the devel packages site soon. Btw, I have great respect for Ben's C code that usually deals very smoothly with the cel files in all sorts of different formats (text or binary, zipped or not), that's definitely no easy job, and has been very well done! Best wishes ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber