Hi again, I've now decided to see how GCRMA performs, I got and installed R-devel and latest BioC (In parallel to R 1.8, so I have r1081 and r1090dev folders in my R directory- but assume this is not the problem?) When I tried to use it I found there is no probe package for the arabidopsis ATH1-121501 chip. I downloaded ATH1-121501_probe_tab.zip from netaffx, changed it to a .gz using win-gz, put it into the matchprobes>data folder and followed the matchprobes vignette and ?makeProbePackage help. I tried this- filename <- file.path(.path.package("matchprobes"), "data", "ATH1-121501_probe_tab.gz") outdir <- tempdir() me <- "Matt Hannah <hannah@nospam>" makeProbePackage("ATH1-121501", datafile = gzfile(filename, open = "r"), outdir = outdir, maintainer = me, version = "0.0.1", force = TRUE) And got this error- Importing the data. Creating package in C:\TEMP\Rtmp11933/ath1121501probe Existing C:\TEMP\Rtmp11933/ath1121501probe was removed. Writing the data. Checking the package. Error in makeProbePackage("ATH1-121501", datafile = gzfile(filename, open = "r"), : Expected but did not find the log-file ath1121501probe.Rcheck/00check.log after R CMD check In addition: Warning message: C:\PROGRA~1\R\RW1090~1/bin/R not found If I add ...check = FALSE) then I suppress the error message but is the ProbePackage ok? Do I just copy the folders from the temp dir to the R library to use it? Does the other warning message matter? Cheers, Matt Dr. Matt Hannah Max-Planck Institute of Molecular Plant Physiology Am M?hlenburg 1 14476 Golm Germany + 49 (331) 567 8255 (phone) + 49 (331) 567 8250 (fax)