Question: Agilent data Read & Normalize
0
gravatar for shawin
4.4 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 • 5.2k views
ADD COMMENTlink modified 4.4 years ago by Gordon Smyth1.5k • written 4.4 years ago by shawin10
2
gravatar for svlachavas
4.4 years ago by
svlachavas640
Greece
svlachavas640 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 4.4 years ago by svlachavas640
2
gravatar for Gordon Smyth
4.4 years ago by
Gordon Smyth1.5k
Australia
Gordon Smyth1.5k wrote:

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

ADD COMMENTlink written 4.4 years ago by Gordon Smyth1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 956 users visited in the last hour