SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Transcriptome wide SNPs based sample clustering chensy RNA Sequencing 0 10-16-2013 08:16 PM

Reply
 
Thread Tools
Old 05-09-2014, 09:05 AM   #1
narges
Member
 
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:

Code:
library(NMF)
Code:
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
Reply

Tags
clustering, nmf, rna-seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:46 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO