[BioC] Affy! From raw data files to Summary expression value without expresso!

Höning, Gunther gunther.hoening at ukmainz.de
Tue Dec 5 14:48:00 CET 2006

Dear list,

I calculated correction values for each probe cell. I do the following:

Reading the cel-files in an AffyBatch:
Expfiles <- c("1.CEL","2.CEL","3.CEL","4.CEL")
chips = ReadAffy(filenames = Expfiles)

Performing background correction:
Chips.bg.mas <- bg.correct(chips, method ="mas")

Performing normalization:
Chips.norm.quantile.mas <- normalize(Chips.bg.mas, method ="constant")

Performing correction
Chips.norm.quantile.mas at exprs <- Chips.norm.quantile.mas at exprs*correctionMAS

### Not done when I tried express.summary.stat..
performing pmcorrection
Chips.PM.Mas <- pmcorrect.mas(Chips.norm.quantile.mas)

And now I want to use the method "computeExprSet" to calculate an ExprSet.

But  I receive the following error:
error in ...... 
        no direct or inherited method for function '...' for this call

The same when I try 

error in express.summary.stat(Chips.norm.quantile.mas, summary = "mas",  : 
        no direct or inherited method for function 'express.summary.stat' for this call

Any ideas ?

Gunther Höning

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