Right I've (with help - thanks Robert, Jean) sorted out what the problem with the ATH1-121501_probe_tab.zip file is - it contains 4 additional control probesets which total 43 probes. The extra probesets are AFFX-r2-At-Actin-3_at (11) AFFX-r2-At-Actin-5_at (11) AFFX-r2-At-GAPDH-3_at (11) AFFX-r2-At-Ubq-5_s_at (10) So this brings me back to my original query which was that I couldn't get the matchprobes package to work on my computer (see other post). So, as the ath1121501probe_1.0 package is wrong is it possible for someone to remove the probesets listed above from the ATH1-121501_probe_tab file and make a new probe package available for download. I would email the file I've modified myself but our institute blocks files >4MB!!!). Alternatively anymore suggestions on how I could get matchprobes to work might help. Also in my emails with robert he suggested to make a general function that could be used by others to compare the probe sequence file and the cdf file (or perhaps even cel files) which would be a useful addition. I'd love to be able to do this but my R skills are sadley lacking (hence all the questions). But before you all volunteer (?) isn't this done to some degree already in the comparewithcdf argument in the getProbeDataAffy function in the matchprobe package? Although evidently from the ATH1 case errors can slip through. And after all this I still haven't got my gcrma done that I thought would be a simple task when I started it over a week ago - anyone would think it was an unlucky day ;-) Thanks Matt

I have made the modified probe package and contributed it. As soon as Jeff gets it up on BioC, you should be able to download it. Please let me know if it works (I know the probes have been removed, but don't have any ath1 cel files to test it with). Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Matthew Hannah" <hannah@mpimp-golm.mpg.de> 02/13/04 11:28AM >>> Right I've (with help - thanks Robert, Jean) sorted out what the problem with the ATH1-121501_probe_tab.zip file is - it contains 4 additional control probesets which total 43 probes. The extra probesets are AFFX-r2-At-Actin-3_at (11) AFFX-r2-At-Actin-5_at (11) AFFX-r2-At-GAPDH-3_at (11) AFFX-r2-At-Ubq-5_s_at (10) So this brings me back to my original query which was that I couldn't get the matchprobes package to work on my computer (see other post). So, as the ath1121501probe_1.0 package is wrong is it possible for someone to remove the probesets listed above from the ATH1-121501_probe_tab file and make a new probe package available for download. I would email the file I've modified myself but our institute blocks files >4MB!!!). Alternatively anymore suggestions on how I could get matchprobes to work might help. Also in my emails with robert he suggested to make a general function that could be used by others to compare the probe sequence file and the cdf file (or perhaps even cel files) which would be a useful addition. I'd love to be able to do this but my R skills are sadley lacking (hence all the questions). But before you all volunteer (?) isn't this done to some degree already in the comparewithcdf argument in the getProbeDataAffy function in the matchprobe package? Although evidently from the ATH1 case errors can slip through. And after all this I still haven't got my gcrma done that I thought would be a simple task when I started it over a week ago - anyone would think it was an unlucky day ;-) Thanks Matt _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I have had mixed success with this new package. The first install I did worked and I was able to compute a GCRMA measure. However when I exited and then restarted R it could load the ath1121501probe library but then when I typed ath1121501probe it said it couldn't find this object. After much trying, including a full R re-install, it seems that when I install from the local zip file it does not extract RData.zip that contains the file called ath1121501probe.rda in the data directory. If I extract this file myself and then start R then it appears to work fine. I'm not sure if this is my computer or the package, but looking at the other win32 probe packages it looks like this one is the only one with the .rda additionally zipped within the zip file. Thanks for providing the probe package anyway. Matt