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}}

Dear Gordon,  I tryed plotMDS.dge function and got good results. But I have two questions:  1. What do "Dimension 1" and "Dimension 2" represent, respectively?  2. I have 12 different samples which were collected from 3 different positions of an organ from 2 species at 2 stages (3*2*2=12 samples). I did RNA-seq and sequenced them in 12 lanes, respectively. I want to see the similarity of the 12 samples by clustering and analyze DE between different species and between different species. Can I separate the 12 samples to 2 groups by the stage or by the species? I'm not sure if I can consider the samples I grouped as "replicates" and use edgeR to do these tasks.  Thanks, Zhe  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:12}}