Question: Agilent Data Normalization Method
0
gravatar for nvayin
4.0 years ago by
nvayin0
United Kingdom
nvayin0 wrote:

I have an Agilent data set , and i normalized and read it using the code bellow , but my result is different from what the paper claim.

library("limma", lib.loc="~/R/win-library/3.1")
targets<-readTargets("target2.txt",row.names=1,sep="")
targets$Filenames[!file.exists(targets$Filenames)]
x <- read.maimages(targets$Filenames,source="agilent", green.only=TRUE)
y <- backgroundCorrect(x,method="normexp")
NormData<-normalizeBetweenArrays(y,method="quantile")

limma agilent • 955 views
ADD COMMENTlink modified 4.0 years ago by Gordon Smyth38k • written 4.0 years ago by nvayin0
Answer: Agilent Data Normalization Method
0
gravatar for Gordon Smyth
4.0 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

It is hard for anyone to help you because you give no indication of what the problem is.

You are using a standard limma package normalization method for Agilent microarray data, so no obvious problem there.

What "paper" are you referring to?

What result do you have that is different from theirs, and why is this a problem?

 

IMPORTANT: Please do not post the same question on more than one mailing list at the same time, as you have done here:

  https://www.biostars.org/p/162449/

This wastes the time of people who might answer you, which is counter-productive as well as impolite.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Gordon Smyth38k

@Gordon - Thank you very much for you reply , i posted on biostar i did not know  there is connection between these two site, iam sorry i will not post twice again. Kindly please can i send you an email with all details ?

ADD REPLYlink written 4.0 years ago by nvayin0
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