dear all: i read the source coding of edgeR_2.4.6 the function of .calcFactorWeighted has some problem .calcFactorWeighted <- function(obs, ref, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10) { if( all(obs==ref) ) return(1) obs <- as.numeric(obs) ref <- as.numeric(ref) nO <- sum(obs) # this is should be the sum of matrix nR <- sum(ref) from the formula in the cited paper, it seems it should be column sum -- 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, I don't see the problem here. Can you elaborate? Why should it be the sum of a matrix? Keep in mind also that this function is run using apply() to each column of the count matrix. Best, Mark On 08.07.2012, at 23:44, wang peter wrote: > dear all: > i read the source coding of edgeR_2.4.6 > the function of .calcFactorWeighted has some problem > > .calcFactorWeighted <- function(obs, ref, logratioTrim=.3, > sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10) { > > if( all(obs==ref) ) > return(1) > > obs <- as.numeric(obs) > ref <- as.numeric(ref) > > nO <- sum(obs) # this is should be the sum of matrix > nR <- sum(ref) > > > from the formula in the cited paper, it seems it should be column sum > -- > 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