[BioC] normalization microarray

[Sean Davis]

On Wed, Sep 14, 2011 at 1:59 PM, Paz Tapia Ramirez
<verotapia at alumnos.utalca.cl> wrote:
>
> Hello, I need to get the normalized values in a file, how I can do that?. I will normalize, but do not know how to visualize the normalized values to a file.
>
> I normalized as follows:
>
> one.col <-list(    R="gMeanSignal",G="gProcessedSignal",
>           Rb="gBGMedianSignal",Gb="gProcessedBackground")
> RG1 <- read.maimages(my.filenames, source="agilent", columns=one.col1, dec=".")
>  RG1 <- backgroundCorrect(RG1, method="half", offset=50)
>  MA <- normalizeBetweenArrays(RG1,method="quantile")

Try something like:

write.table(MA$M,file="mydata.txt",sep="\t")

Sean