Hi Ming, voom is part of the limma package. There is a voom case study in the limma User's Guide with complete working code. It is the last case study in the users guide. voom works fine with either counts, or fractional counts, or scaled counts. We are currently finalizing additional voom code to detect differential splicing. That code isn't in the public package, but will be soon. Best wishes Gordon On Thu, 30 Jan 2014, Ming Yi wrote: > I found the following documents > > http://stuff.mit.edu/afs/athena/software/r/r_v2.15.1/lib/R/library/l imma/html/voom.html > http://www.bioconductor.org/packages/release/bioc/vignettes/limma/in st/doc/usersguide.pdf > http://www.statsci.org/smyth/pubs/VoomPreprint.pdf > > But I could not find the real limma-voom package document. Is voom just > as normalization function prior to using limma linear model? Any good > examples of case study of working commands available as example? > > Thanks again! > Ming ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Hi, Dr. Smyth: Thanks for the info. I used limma a lot but not much on voom. I will give a shot on voom. Thanks again and best Ming > Date: Thu, 30 Jan 2014 13:05:57 +1100 > From: smyth@wehi.EDU.AU > To: yi02@hotmail.com > CC: bioconductor@r-project.org > Subject: limma-voom > > Hi Ming, > > voom is part of the limma package. There is a voom case study in the > limma User's Guide with complete working code. It is the last case study > in the users guide. > > voom works fine with either counts, or fractional counts, or scaled > counts. > > We are currently finalizing additional voom code to detect differential > splicing. That code isn't in the public package, but will be soon. > > Best wishes > Gordon > > On Thu, 30 Jan 2014, Ming Yi wrote: > > > I found the following documents > > > > http://stuff.mit.edu/afs/athena/software/r/r_v2.15.1/lib/R/library /limma/html/voom.html > > http://www.bioconductor.org/packages/release/bioc/vignettes/limma/ inst/doc/usersguide.pdf > > http://www.statsci.org/smyth/pubs/VoomPreprint.pdf > > > > But I could not find the real limma-voom package document. Is voom just > > as normalization function prior to using limma linear model? Any good > > examples of case study of working commands available as example? > > > > Thanks again! > > Ming > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:9}}