Hi all, I'm trying out the vsn procedure instead of rma. But i got the following error message. What does "ARG" mean? Must the VSN procedure be used with no background correction? and why is there a warning saying that "multiget is deprecated? I installed the R vers.1.9.0 and BioC 1.4. I appreciate all the help that you can give me, Edmund > eset <- expresso(Data, bgcorrect.method = "mas", normalize.method = "vsn", pmcorrect.method = "pmonly", summary.method = "medianpolish") background correction: mas normalization: vsn PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...Error in match.arg(method, normalize.AffyBatch.methods) : ARG should be one of constant, contrasts, invariantset, loess, qspline, quantiles, quantiles.robust In addition: Warning messages: 1: 'multiget' is deprecated. Use 'mget' instead. See help("Deprecated") and help("base-deprecated"). 2: 'multiget' is deprecated. Use 'mget' instead. See help("Deprecated") and help("base-deprecated"). >

You are getting an error because you haven't added vsn to the affybatch normalization methods (this is covered in the help for normalize.affybatch.vsn). Do this first: normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") Then run expresso. HTH, 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 >>> Edmund Chang <echang4@life.uiuc.edu> 06/03/04 03:03PM >>> Hi all, I'm trying out the vsn procedure instead of rma. But i got the following error message. What does "ARG" mean? Must the VSN procedure be used with no background correction? and why is there a warning saying that "multiget is deprecated? I installed the R vers.1.9.0 and BioC 1.4. I appreciate all the help that you can give me, Edmund > eset <- expresso(Data, bgcorrect.method = "mas", normalize.method = "vsn", pmcorrect.method = "pmonly", summary.method = "medianpolish") background correction: mas normalization: vsn PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...Error in match.arg(method, normalize.AffyBatch.methods) : ARG should be one of constant, contrasts, invariantset, loess, qspline, quantiles, quantiles.robust In addition: Warning messages: 1: 'multiget' is deprecated. Use 'mget' instead. See help("Deprecated") and help("base-deprecated"). 2: 'multiget' is deprecated. Use 'mget' instead. See help("Deprecated") and help("base-deprecated"). > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

You have to add the following line before you can use vsn as a normalization method. normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") Isaac Edmund Chang wrote: > Hi all, > I'm trying out the vsn procedure instead of rma. But i got the > following error message. What does "ARG" mean? > Must the VSN procedure be used with no background correction? and why > is there a warning saying that "multiget is deprecated? > I installed the R vers.1.9.0 and BioC 1.4. > > I appreciate all the help that you can give me, > Edmund > > > eset <- expresso(Data, bgcorrect.method = "mas", normalize.method = > "vsn", pmcorrect.method = "pmonly", summary.method = "medianpolish") > background correction: mas > normalization: vsn > PM/MM correction : pmonly > expression values: medianpolish > background correcting...done. > normalizing...Error in match.arg(method, normalize.AffyBatch.methods) : > ARG should be one of constant, contrasts, invariantset, loess, > qspline, quantiles, quantiles.robust > In addition: Warning messages: > 1: 'multiget' is deprecated. > Use 'mget' instead. > See help("Deprecated") and help("base-deprecated"). > 2: 'multiget' is deprecated. > Use 'mget' instead. > See help("Deprecated") and help("base-deprecated"). > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor