[BioC] edgeR: exactTest different p value in new version 2.4

[Gordon K Smyth]

You can also type

   news(package="edgeR")

at the R prompt to see the same information.

Best wishes
Gordon


On Fri, 18 Nov 2011, Gordon K Smyth wrote:

> Dear Sermsawat,
>
> Yes, see the entry for edgeR in:
>
>  http://www.bioconductor.org/news/bioc_2_9_release/
>
> which says
>
> "A choice of rejection regions is now implemented for exactTest, and the 
> default is changed from one based on small probabilities to one based on 
> doubling the smaller of the tail probabilities. This gives better results 
> than the original conditional test when the dispersion is large (especially > 
> 1). A Beta distribution approximation to the tail probability is also 
> implemented when the counts are large, allowing exactTest() to be much faster 
> and use less memory."
>
> Best wishes
> Gordon
>
> ---------------------------------------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> Tel: (03) 9345 2326, Fax (03) 9347 0852,
> smyth at wehi.edu.au
> http://www.wehi.edu.au
> http://www.statsci.org/smyth
>
> On Fri, 18 Nov 2011, Sermsawat Tunlaya-anukit wrote:
>
>> I used edgeR to test differential expression of RNA seq data, but i noticed 
>> some different between old version 2.2.5and new version2.4. I compare p 
>> value and adjust p value between old version and new one using exactTest() 
>> and found that the values are slightly different(logFC and LogConc are the 
>> same). Do you change method to calculate p value in the new version?
>> 
>> Best regards,
>> Sermsawat Tunlaya-anukit
>

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