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Transcriptome wide SNPs based sample clustering chensy RNA Sequencing 0 10-16-2013 08:16 PM

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Old 05-09-2014, 09:05 AM   #1
Location: Finland

Join Date: Aug 2012
Posts: 29
Default RNA-seq sample clustering using NMF package

I want to cluster RNA-seq samples (417 samples) using based on the expression levels of a group of selected genes using NMF method. Having a matrix (mat) of expression levels with sample names as columns and gene names as rows I tried following command from Bioconductor NMF package:

res <- nmf(mat, 2:10, nrun = 200, seed = 123456)
I figure out that rank=4 is the optimum.
First do you think it is a reasonable way of sample clustering?
If so, should I normalize/transform the expression levels before clustering (like TMM normalization or log or asinh transformations)?
And finally, I need to know the names of samples in each calculated clusters. Using command "basisnames" I got NULL. What command should I try to get the samples orders in clusters?

Thanks for the help.
narges is offline   Reply With Quote

clustering, nmf, rna-seq

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