Agilent data Read & Normalize

Question

[shawin]

I have an Agilent dataset, I am trying to read and normalize it, I used the code bellow but I am getting error.

library(limma)
targets <- readTargets("targets_limma.txt", row.names=1,sep ="")
x <- read.maimages(targets$Filename,source="agilent",green.only=TRUE)

Can we use RMA tp normalize Agilent data?

NormData<-rma(data) does not work.

Please any help

Answer 1

[svlachavas]

Dear Shawinkarim,

You should consider reading limma users guide: case 17.4 for agilent-page 110 (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf)

It has a detailed pipeline for handling agilent data. Just check the function: ?normalizeBetweenArrays

which states that the default option for single channel agilent microarrays is "quantile normalization"

Hope that helps,
Efstathios

Answer 2

[Gordon Smyth]

rma() is only for Affymetrix microarray data, which you do not have.