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

James W. MacDonald jmacdon at med.umich.edu
Tue Dec 5 15:11:54 CET 2006

Hi Gunther,

The problem with doing your own method is that you have to watch closely 
what you are doing, and be very familiar with the help pages.

The Höning wrote:
> 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 sure what correctionMAS is here, but let's assume it is either a 
scalar or a vector.

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

Now if you do class(Chips.PM.Mas), you will get 'matrix'.

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

Unfortunately, the arguments for computeExprSet are

x: a 'AffyBatch' holding the probe level informations to
           generate the expression values.

But you are passing a matrix, hence you get the following error.
> 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

Again, the help page for this function states:


        x: a ('ProbeSet'

But you are passing an AffyBatch, not a ProbeSet. NB - this is an old 
function (as are all functions that take a ProbeSet as their input), and 
may not work as intended any longer.

Most of the 'roll-your-own' functions in the affy package were developed 
in the days when people were still arguing over the best method to use 
for affy data. In the intervening time it appears (to me at least) that 
people have settled on their favorite method, so these legacy functions 
are no longer used as much and hence might not be maintained as 
rigorously as e.g., rma(). In fact, last I heard Rafa was considering 
taking expresso() and friends out of the affy package because they don't 
appear to be used much, and are a pain to maintain.



> Any ideas ?
> Gunther Höning
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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