I have downloaded the Michigan Lung cancer dataset celfiles from the CAMDA 2003 Conference Contest Datasets, for testing a survival analysis. ( http://www.camda.duke.edu/camda03/datasets/ ) When I tried to perform gcrma(), I got into memory problems so I tried just.gcrma(), but this caused the following error: Computing affinities..Done. Adjusting for optical effect................................................................ ...... ...........................Done. Adjusting for non-specific binding.Error in quantile.default(y, Q) : Missing values and NaN's not allowed if `na.rm' is FALSE This same error appears when performing this on much smaller subsets, with which gcrma() has no problem Used Versions Windows 2000 R 1.9 gcrma 1.0.6 Jan

That's a bug in just.gcrma. I am going to commit the bugfix to BioC momentarily, but it will take a while to propagate to the BioC website. In the interim, you can source the attached file before running just.gcrma(). 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 >>> "Oosting, J. (PATH)" <j.oosting@lumc.nl> 04/22/04 08:04AM >>> I have downloaded the Michigan Lung cancer dataset celfiles from the CAMDA 2003 Conference Contest Datasets, for testing a survival analysis. ( http://www.camda.duke.edu/camda03/datasets/ ) When I tried to perform gcrma(), I got into memory problems so I tried just.gcrma(), but this caused the following error: Computing affinities..Done. Adjusting for optical effect................................................................ ...... ...........................Done. Adjusting for non-specific binding.Error in quantile.default(y, Q) : Missing values and NaN's not allowed if `na.rm' is FALSE This same error appears when performing this on much smaller subsets, with which gcrma() has no problem Used Versions Windows 2000 R 1.9 gcrma 1.0.6 Jan _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... Name: justGCRMA.R Type: application/octet-stream Size: 13260 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040422/06fdea71/justGCRMA-0001.obj