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Elaine yang wrote: > Hi there, I am new in using package and some basic questions for > ReadAffy. I tried to use ReadAffy(widget=TRUE) function to select the > cel files by using widget tools. But after I select all the cel > files, it goes to create the phenodata step. What's the meaning of > "covar" and how to choose the value of covariate? The covariate is a descriptive term used to distinguish one sample from another. For instance, let's say you have an experiment where you are comparing rat liver tumors vs normal liver after treatment with a chemotherapeutic agent. You would have (at least) two covariate names here. An example of what the covariates would look like is this: Sample Treatment Type 1 Chemo Tumor 2 Chemo Normal 3 None Tumor 4 None Normal Does that help? Best, Jim > > Thanks in advance! > > Elaine > > __________________________________________________ > > > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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