[BioC] Using proportions...

Wolfgang Huber whuber at embl.de
Thu Nov 17 15:56:53 CET 2011

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

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
> http://www.embl.de/research/units/genome_biology/huber
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Wolfgang Huber

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