There are of course several other papers on this topic authored by people on this list and by contributors to Bioconductor, e.g. a particularly placative one: Nat Biotechnol. 2011 Jul 11;29(7):572-3. doi: 10.1038/nbt.1910. Sequencing technology does not eliminate biological variability. Hansen KD, Wu Z, Irizarry RA, Leek JT. Best wishes Wolfgang On 11/17/11 3:45 PM, Wolfgang Huber wrote: > On 11/17/11 4:58 AM, Jim Silverton wrote: >> Hello, >> Just wanted to find out why in a RNA-seq with treatment and control, no >> one does the two sample proportion comparison for two features. The total >> reads are large so it should work asymptotically. >> > > Dear Jim > > lots of people do, but generally the answer that you get is not what one > is looking for, because such an analysis tests against (and too > frequenly rejects) an uninteresting null hypothesis. Have, for instance, > a look at http://genomebiology.com/2010/11/10/R106 . > > Best wishes > Wolfgang > > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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