dear all: i have two questions 1. is the "size factor" from DESeq equally to the "norm factor" in the edgeR 2. i can get the normalized counts by counts(obj,normalized=T) how to get normalized counts from edgeR can i use the each col of count matrix divided by norm factor -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

Hi Shan, On 09.07.2012, at 05:05, wang peter wrote: > dear all: > i have two questions > > 1. is the "size factor" from DESeq equally to the "norm factor" in the edgeR No. In edgeR, the library size and additional normalization scaling factors are separated. See the two different columns in the $samples element of a 'DGEList' object: > d$samples group lib.size norm.factors sample.1 1 12367 0.9746280 sample.2 1 12088 1.0243994 sample.3 2 12823 0.9897893 sample.4 2 12374 1.0119267 In all the downstream code, the lib.size and norm.factors are multiplied together to act as the effective library size; this (product) would be similar to DESeq's size factor. > 2. i can get the normalized counts by > > counts(obj,normalized=T) > > how to get normalized counts from edgeR > can i use the each col of count matrix divided by norm factor In edgeR, you can use cpm(). For example: d <- DGEList(counts=...) nc <- cpm(d, normalized.lib.sizes=FALSE) You might have a skim through the edgeR user's guide; many of these concepts are described in more detail there. Best, Mark > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin ---------- http://www.fgcz.ch/Bioconductor2012