[BioC] (no subject)

[David Ruau]

Dear useR,

I use R 2.5.0 since it's release and so for no problem... to I had to  
re-process some data and I encounter a problem while trying to use  
the mas5 function from the affy package:

 > da.26may.mas5 <- mas5(da.26may, sc=300)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
12625 ids to be processed
|                    |
|Error in update.default(pbt) : need an object with call component
In addition: Warning message:
$ operator not defined for this S4 class, returning NULL in: object$call

 > traceback()
8: stop("need an object with call component")
7: update.default(pbt)
6: update(pbt)
5: .local(x, pmcorrect.method, summary.method, ...)
4: computeExprSet(afbatch, summary.method = summary.method,  
pmcorrect.method = pmcorrect.method,
        ids = summary.subset, summary.param = summary.param,  
pmcorrect.param = pmcorrect.param)
3: computeExprSet(afbatch, summary.method = summary.method,  
pmcorrect.method = pmcorrect.method,
        ids = summary.subset, summary.param = summary.param,  
pmcorrect.param = pmcorrect.param)
2: expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas",
        normalize = FALSE, summary.method = "mas", ...)
1: mas5(da.26may, sc = 300)

 > sessionInfo()
R version 2.5.0 Patched (2007-04-26 r41343)
i386-apple-darwin8.9.1

locale:
C

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

other attached packages:
    hgu95av2 hgu95av2cdf        affy      affyio     Biobase
    "1.16.0"    "1.16.0"    "1.14.1"     "1.4.0"    "1.14.0"

---
David Ruau
Institute for Biomedical Engineering
RWTH Aachen