[BioC] marray or rma?

[Adaikalavan Ramasamy]

'marray' is a package designed for spotted two color arrays.

rma is a function in the 'affy' package which is designed for Affymetrix
chips. If your data is affymetrix, then you need the CEL files and
something along this line :

setwd("/path/to/cel/files") 
# change working dir OR you can use the option filenames in ReadAffy()

raw <- ReadAffy()
out <- rma(raw)
expressionValues <- exprs(out)
       
write.table( expressionValues, file="out.txt", sep="\t", quote=FALSE)

This will get you the expression values in a matrix format.

Regards, Adai.


On Sat, 21 Feb 2004 gjam at daimi.au.dk wrote:

> Hi,
> I don't know the difference between the use of the 'marray' package and the use
> of the function 'rma'. I would like to calculate the expression from raw data
> and to normalize all the data afterward.
> Thanks for your help,
> Jamila
> 
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