Lana you would lose a lot of power when you apply edgeR on the per-base coverage, since the numbers will be much smaller than the numbers summed up by feature. Also, multiple testing could be a bigger problem, and the redundancy seems clunky (neighboring bases' coverage is highly correlated). Best wishes Wolfgang Sean Davis scripsit 05/18/2011 07:49 PM: > Hi, Lana. > > I would think that would make a difference since what you want to finally be > using are the counts of "molecules". > > Sean > > > On Wed, May 18, 2011 at 1:45 PM, Lana Schaffer<schaffer at="" scripps.edu=""> wrote: > >> Hi, >> I used the raw counts which are a coverage for each base within feature. >> Does it make any significant difference to use this raw count rather than >> The read count ? >> >> Lana Schaffer >> Biostatistics, Informatics >> DNA Array Core Facility >> 858-784-2263 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber