[BioC] Clustering RNA-seq profiles using edgeR

[Gordon K Smyth]

Dear Zhe,

To do clustering of RNA-seq profiles using the edgeR packages, you can use 
the plotMDS.dge function.  See the User's Guide for examples.  This 
function is already designed for RNA-seq data, so there is no need to 
worry about normalization factors or variance stabilizing transformations 
etc.

Best wishes
Gordon


[BioC] edgeR normalization factors
zhedianyou at yahoo.cn
Mon Jun 28 05:19:19 CEST 2010

Hello,

I have a question about using TMM normalization factors. I want to modify 
the count for each gene after normalization. Should I just need to divide 
the count of each gene by the normalization factor for its library? Then, 
I may use the normalized data for DE analysis and other further analysis 
(e.g. clustering).

Thanks a lot,
Zhe

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}