Agilent data Read & Normalize
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
2 answers
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
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svlachavas
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rma() is only for Affymetrix microarray data, which you do not have.
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