Question: microarray agilent data
gravatar for evoke
4.2 years ago by
European Union
evoke0 wrote:


I have a question about my agilent microarray data.

It includes  before & after infection data of the same individuals and also replicates of non-infected other individuals as a kind of  control to these infected ones . There are 15 individuals and thus 30 microarray files. I am using "limma" package to read and normalize them. However, i have doubts if i should use the codes below to identifiy genes differently expressed, because when i cluster the datasets, the replicates do not group together:


RG_2= backgroundCorrect(z, method="minimum")
MA.exp= normalizeBetweenArrays(RG_2)
MA.exp_log= log(MA.exp$E)

SibShip = factor(targets_paired$SibShip)
Treat = factor(targets_paired$Treatment, levels=c("Not Inf.","Infected"))
design = model.matrix(~SibShip+Treat)
fit = lmFit(MA.exp_log, design)
fit = eBayes(fit)
topTable(fit, coef="TreatInfected")

In this case, should I analyze the data by just grouping as Infected & Non-infected?

Thank you in advance.


microarray limma agilent • 633 views
ADD COMMENTlink modified 4.2 years ago by arfranco130 • written 4.2 years ago by evoke0
Answer: microarray agilent data
gravatar for arfranco
4.2 years ago by
European Union
arfranco130 wrote:

According limma, you need to go through one within and between normalization if using two color arrays, or a single normalization if using a single color. You need to provide with this information, and also with the targets definition

ADD COMMENTlink written 4.2 years ago by arfranco130

One more thing, Why are you doing the MA.exp_log step ?

Have you read that in the limma reference document?. I don't think you need to do it, and if a log is calculated, it should be in base 2

ADD REPLYlink written 4.2 years ago by arfranco130
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