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List:       bioconductor
Subject:    [BioC] Clustering RNA-seq profiles using edgeR
From:       Gordon K Smyth <smyth () wehi ! EDU ! AU>
Date:       2010-06-30 23:11:01
Message-ID: Pine.WNT.4.64.1007010906380.5848 () PC602 ! alpha ! wehi ! edu ! au
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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

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