[BioC] plier error message

James W. MacDonald jmacdon at med.umich.edu
Mon Feb 12 21:19:19 CET 2007

Karen Vranizan wrote:
> Hello. What does the following error message mean?  It is a result of
> running justPlier on an affybatch set of 9 chips.  I am using R 2.4.0
> and plier 1.5.1.  Thank you.

It means that you installed a devel version of plier on a release 
version of R. Unfortunately with evolving software like R and BioC, 
mixing and matching things like that can have unintended consequences.

The usual prescription is best - use biocLite() to install packages so 
you don't get mismatches.



>> plierset<-justPlier(data,normalize=T)
> Quantile normalizing...Done. Error in function (classes, fdef,
> mtable)  : unable to find an inherited method for function
> "experimentData", for signature "AffyBatch" In addition: Warning
> message: updating phenoData argument to 'AnnotatedDataFrame'
> Karen Vranizan Functional Genomics Lab 261A Life Sciences Addition 
> Mail Code #3200 UC Berkeley, CA 94720-3200
> Phone: 510-642-7520 Fax:      510-643-2685 email:
> vranizan at berkeley.edu
> [[alternative HTML version deleted]]
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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