hello all In the edgeR package? the lib.size: vector of length ncol(counts) giving the total number of reads sequenced for each sample. If not separately provided, will be set to colSums(counts). but there are three different concepts. usually the number of mapped reads < total reads < counts because not all of the reads can be mapped and one mapped reads have more than 1 hit. so which one should be used in the NB model? -- 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, We typically use a fourth concept, the notion of 'effective' library size. The idea is quite simple, and spelled out here: http://genomebiology.com/2010/11/3/R25 And, the function is implemented in edgeR's calcNormFactors(). HTH, Mark On 12.12.2011, at 17:44, wang peter wrote: > hello all > > > In the edgeR package? > the lib.size: vector of length ncol(counts) giving the total number > of reads sequenced > for each sample. If not separately provided, will be set to colSums(counts). > > but there are three different concepts. > > usually the number of mapped reads < total reads < counts > because not all of the reads can be mapped > and one mapped reads have more than 1 hit. > > so which one should be used in the NB model? > > -- > 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: Y32-J-34 w: http://tiny.cc/mrobin