Dear Bioconductor List, I am processing Affymetrix Mouse ST1.0 Gene chips with oligo. The first quantile line doesn't seem to be visible on the NUSE and RLE plots. In my past experience with NUSE and RLE plots for Mous2 430.2 chips, the second quantile line was visible. Here it is not. I am wondering if this is a property of ST1.0 chips in general, a bug in the NUSE program for this class of chips, or is indicative of a problem with this dataset. This last option is especially important, as I have not observed statistically significant differential expression with this dataset. I would greatly appreciate it if someone more experienced with ST1.0 Gene chips and oligo than myself could at the plots. If anyone can look at them I will send them offline. My script is: plm<-fitPLM(raw) png("NUSE.png") boxplot(plm,ylim=c(0.9,1.1),main="NUSE") dev.off() png("NUSEfull.png") boxplot(plm,main="NUSE") dev.off() png("RLE.png") boxplot(plm,ylim=c(0.9,1.1),main="RLE") dev.off() png("RLEfull.png") boxplot(plm,main="RLE") dev.off() My session is (at I hope that using R2.13.0 is not a problem: R version 2.13.0 (2011-04-13) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.8.1 pd.mogene.1.0.st.v1_3.2.0 RSQLite_0.9-4 DBI_0.2-5 [5] oligo_1.16.2 preprocessCore_1.14.0 oligoClasses_1.14.0 Biobase_2.12.1 loaded via a namespace (and not attached): [1] affxparser_1.24.0 affyio_1.20.0 Biostrings_2.20.0 bit_1.1-7 ff_2.2-3 [6] IRanges_1.10.0 splines_2.13.0 Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ I am a Bayesian. When I see a multiple-choice question on a test and I don't know the answer I say "eeney-meaney-miney-moe". Rose Friedman, Age 14