normalization on microarray

Question

[minni9234]

Can someone help me on normalization of microarray. My output before using a limma packages are below. However, I don't know how to perform using normalizeWithinArrays() if the class of the data is a matrix format. Also, what command I should use to find out how many genes going up in siMLL2 at padj < 0.1 and abs(logFC)>1?

> head(selExpr,5)
             GSM921888 GSM921889 GSM921890 GSM921891
OR4F17         24.3536   24.6945   18.6882   20.6363
LOC100134822 2004.2300 1959.5600 1590.9400 1534.8100
OR4F29         40.3611   42.6291   48.8858   32.3297
LOC100287934  286.6540  253.0200  320.1410  275.0030
FAM87A        172.6980  182.9510  210.9790  226.7940

samples <- as.factor(c("scr", "scr", "siMLL2", "siMLL2")) #convert into factors
design<-model.matrix(~0+samples) #set up the experimental design
colnames(design)<-levels(samples)

fit<-lmFit(selExpr,design)
contrast.matrix<-makeContrasts(siMLL2 - scr, levels=design)
fits<-contrasts.fit(fit,contrast.matrix)
ebfit<-eBayes(fits)
topTable(ebfit,number=50,coef=1)

[Devon Ryan]

Those values are already normalized. You can even analyze them directly from GEO (click on the GEO2R link on GEO), which can also show you the script it uses. Anyway, just download the .CEL files if you want to analyze things yourself. You have MUCH better control of things that way.

[minni9234]

Thanks Ryan. How do I know if the data is already normalized? Do you know if there is a command after

"topTable(ebfit,number=50,coef=1)" that I can use to analyze the amount of genes going up in siMLL2 at padj < 0.1 and abs(logFC)>1?

[Devon Ryan]

I'm guessing that you downloaded the series matrix file and clicking on one of the individual samples would show you that the values are already normalized (it explicitly says that). topTable returns a dataframe, so just with(tt, which(padj<0.1 & abs(logFC)>1)) where tt is the output from topTable.