[BioC] Illumina based one color microarray data analysis

[Wei Shi]

Dear KaushalRaj,

The heatmap.2 function in gplots package is a useful tool for making heatmaps. But I can't see how you normalized your data from your provided code. The neqc function in limma can be used to background correct and normalize your illumina data.

Hope this helps.

Cheers,
Wei

On Sep 4, 2013, at 12:23 PM, KaushalRaj Chaudhary [guest] wrote:

> 
> 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)
> 
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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