﻿﻿﻿﻿Hello
 Dear all
 I have a question about topTable in limma package. Can i specify
parameters of interest in
 topTable, i.e. it gives me specific parameters such as adj.P-value
and logFC, not ID and names
 columns because both of them are caused to disorder output file of
topTable. I would like to
 process our data in excel

 limma(library)
 ﻿﻿﻿﻿targets=readTargets("ApoAITargets.txt")
 RG=read.maimages(targets$FileName, source="spot")
 MA=normalizeWithinArrays(RG, method="loess")
 controlRef=rep(1,16)
 KOcontrol=c(rep(0,8),rep(1,8))
 design=cbind(controlRef,KOcontrol)
 fit=lmFit(MA,design)
 fit=eBayes(fit)
 option(digits=3)
 result=topTable(fit, coef=2, number=6384, adjust="BH")
 as.matrix(result)
 write.csv(result,file="printtiploess.csv", quote=FALSE, col.names=TRUE,
 sep=",")

 Regards

-- 
*S. Fazeli
MSc Student of Chem. Eng.
ferdowsi University
mashhad
Iran*

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