Question: Agilent data Read & Normalize
0
gravatar for shawin
3.6 years ago by
shawin10
United Kingdom
shawin10 wrote:

I have an Agilent dataset , iam 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

R • 4.5k views
ADD COMMENTlink modified 3.5 years ago by Gordon Smyth750 • written 3.6 years ago by shawin10
2
gravatar for svlachavas
3.6 years ago by
svlachavas560
Greece
svlachavas560 wrote:

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

ADD COMMENTlink written 3.6 years ago by svlachavas560
1
gravatar for Gordon Smyth
3.5 years ago by
Gordon Smyth750
Australia
Gordon Smyth750 wrote:

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

ADD COMMENTlink written 3.5 years ago by Gordon Smyth750
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