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2 hours ago by


Hi I am analyzing microarray under agilent platform. I used following codes

workDir<- "home/dare_devil/arrays/data1"

annotation <- read.table(file.path(workDir, "annotation.txt"), 
                        header = TRUE, sep = 't', quote = "",
                        stringsAsFactors = FALSE)
if (length(unique(annotation$Name)) != nrow(annotation)) {stop("The names in the annotation file must be unique!")}

rawData <- read.maimages(unique(file.path(workDir, annotation$File)),
                        source = "agilent", green.only = TRUE,
                        names = annotation$Name, annotation = c("ProbeName"))

# correct, normalize, and extract
bgData <- backgroundCorrect(rawData)
normData <- normalizeBetweenArrays(bgData, method = "quantile")
normEset <- normData$E; rownames(normEset) <- normData$genes$ProbeName

#create design
conditions<- paste(annotation$Group)
conditions <- factor(conditions, levels=unique(conditions))
design <- model.matrix(~0+ conditions)
colnames(design) <- levels(conditions)

#fit the design
fit <- lmFit(normEset, design)
#Make contrast
contrast.matrix <- makeContrasts(Grp1 - Grp2, levels=design)

#Fit contrast
fit.cont<-, contrast.matrix)
#ebayes Fit
fit.cont<- eBayes(fit.cont)

#check the results

I got following results

      Grp1 - Grp2
Down             0
NotSig       62948
Up               0

But after running the code I did not get any significant genes. Am I doing anything wrong?

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