Agilent Data Normalization Method
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nvayin • 0
@nvayin-9005
Last seen 5.9 years ago
United Kingdom

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 • 1.2k views
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@gordon-smyth
Last seen 9 hours ago
WEHI, Melbourne, Australia

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.

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@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 ?

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