[BioC] justGCRMA problem :(

Cecile Laurent cecile.laurent at curie.fr
Mon Oct 27 14:36:25 CET 2008

Dear BioC,

I've just updated R (2.8) and bioconductor (2.3), and justGCRMA function 
doesn't work :

 > sessionInfo()
R version 2.8.0 (2008-10-20)


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
[1] gcrma_2.14.0       matchprobes_1.14.0 affy_1.20.0        

loaded via a namespace (and not attached):
[1] affyio_1.10.0        preprocessCore_1.4.0

 > require(gcrma)
 > celfile.path <- 
 > filenames <- list.celfiles(path=celfile.path, full.names=FALSE)
 > normData <- justGCRMA(filenames=filenames, celfile.path=celfile.path, 
type="affinities", fast=TRUE)
Computing affinities.Done.
Adjusting for optical effect..............Done.
Adjusting for non-specific binding.............Done.
Erreur dans just.gcrma(filenames = l$filenames, phenoData = l$phenoData,  :
  INTEGER() can only be applied to a 'integer', not a 'environment'

Any idea of what is going wrong with the new version?

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