[BioC] vsn procedure error

James MacDonald jmacdon at med.umich.edu
Thu Jun 3 21:21:24 CEST 2004

You are getting an error because you haven't added vsn to the affybatch
normalization methods (this is covered in the help for

Do this first:

normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")

Then run expresso.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Edmund Chang <echang4 at life.uiuc.edu> 06/03/04 03:03PM >>>
Hi all,
I'm trying out the vsn procedure instead of rma. But i got the
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,

 > 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").

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