[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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