Question: raw counts for edgeR
0
gravatar for Lana Schaffer
8.4 years ago by
Lana Schaffer1.3k
Lana Schaffer1.3k 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]]
coverage • 631 views
ADD COMMENTlink modified 8.4 years ago by Sean Davis21k • written 8.4 years ago by Lana Schaffer1.3k
Answer: raw counts for edgeR
0
gravatar for Sean Davis
8.4 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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@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@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]]
ADD COMMENTlink written 8.4 years ago by Sean Davis21k
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
ADD REPLYlink written 8.4 years ago by Wolfgang Huber13k
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