Dear Pedro and list I encountered an error message upon filtering an RMA normalized object. > ddPROC=filterMicroRna(agiMicro.rma, + agiMicroraw, + control=TRUE, + IsGeneDetected=FALSE, + wellaboveNEG=FALSE, + limIsGeneDetected=50, + limNEG=25, + makePLOT=TRUE, + targets, + verbose=TRUE) FILTERING PROBES BY FLAGS FILTERING BY ControlType Error in data.frame(as.character(PROBE_ID), as.character(GENE_ID), as.character(probe.chr), : arguments imply differing number of rows: 644, 0 The relevant portions of my script up until that point are: ################################################### library("AgiMicroRna") targets<-readTargets("Targets.txt",verbose=TRUE) agiMicroraw<-readMicroRnaAFE(targets,verbose=TRUE) agiMicro.rma=rmaMicroRna(agiMicroraw,normalize=TRUE,background=FALSE) ddPROC=filterMicroRna(agiMicro.rma, agiMicroraw, control=TRUE, IsGeneDetected=FALSE, wellaboveNEG=FALSE, limIsGeneDetected=50, limNEG=25, makePLOT=TRUE, targets, verbose=TRUE) ################################################### Please advise. 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/ In Memoriam, George Scithers