[BioC] expresso problem

[Jianping Jin]

Hi Bioconducter:

I ran expresso of Affy package on R version 2.1.0 as below:

>  dataRMA_norm_loess <- expresso(data, bgcorrect.method="rma",
+ normalize.method="loess", pmcorrect.method="pmonly", 
summary.method="medianpolish")

The error message I got was:

background correction: rma
normalization: loess
PM/MM correction : pmonly
expression values: medianpolish
background correcting...Error in bg.correct(afbatch, method = 
bgcorrect.method) :
        no direct or inherited method for function 'bg.correct' for this 
call

If I ran with bg.correct="rma" and left the rest the same, I got:

Error in expresso(data, bg.correct = "rma", normalize.method = "loess",  :
        unimplemented type 'character' in 'asLogical'

Note: data is the loaded .CEL files from the estrogen package as well as 
the phenotypic data.

Anything wrong?

Thanks!

JP-


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x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
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x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
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