[BioC] Illumina based one color microarray data analysis

[KaushalRaj Chaudhary [guest]]

Hi,  
I have a one color illumina microarray dataset with six samples (3 wild type and 3 mutant types ) on the columns and around 48000 genes on the rows of excel.  I want to get the hierarchical clustering of genes but I am getting clustering of samples only. Can I use limma package for the analysis of this data and also get heatmap.  The data is already normalized.  Thank you very much for your help.

Regards,

 -- output of sessionInfo(): 

data1=as.matrix(read.csv("kamesh.csv", header=T))
data2=log(data1)
dim(data2)
class(data2)
data3=data2[,-1]
head(data3)
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("limma")
biocLite("lumi")

hist(data3)
boxplot(data3)
xdist <- dist(t(data3))
dim(t(data3))
hc <- hclust(xdist)
plot(as.dendrogram(hc))
image(data2)



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