[BioC] raw counts for edgeR

[Wolfgang Huber]

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
>>
>>
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-- 


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