[BioC] edgeR exactTest dispersion value of 0 gives error

[Gordon K Smyth]

Dear Surjyendu Ray,

In my experience, exactTest() does not give an error for dispersion=0, as 
the reproducible code example below shows.  If you believe there is a 
problem, please provide an example of code that I can run that will 
reproduce the error message.  Please see the posting guide (third 
paragraph of "Preparing"):

   http://www.bioconductor.org/help/mailing-list/posting-guide/

Best wishes
Gordon

> example(exactTest)
> topTags(exactTest(d,dispersion=0))
Comparison of groups:  2-1
              logFC   logCPM       PValue         FDR
Gene.18 -2.2658941 12.87267 0.0003249142 0.004719867
Gene.2   1.8744691 13.21371 0.0004719867 0.004719867
Gene.13 -1.8002305 12.96578 0.0021024016 0.014016010
Gene.16  1.4947647 12.91998 0.0106738405 0.053369203
Gene.19 -0.8400591 13.77314 0.0440465461 0.176186184
Gene.1   0.7182290 13.89652 0.0721774385 0.240591462
Gene.3  -0.4117248 13.94306 0.3135030533 0.884136677
Gene.5  -0.4786536 13.13571 0.4050322461 0.884136677
Gene.8   0.3658714 13.74714 0.4187541883 0.884136677
Gene.17  0.5305147 12.72067 0.4420683384 0.884136677
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252 
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] edgeR_2.6.10        limma_3.13.15       BiocInstaller_1.4.7

loaded via a namespace (and not attached):
[1] tools_2.15.1




On Tue, 7 Aug 2012, Surjyendu Ray wrote:

> Dear Sir,
>             I have tried out the procedure using the latest version of R
> and edgeR, however, I am still getting the same error. Please advise.
>           Thanking you,
>                                     Yours faithfully,
>                                     Surjyendu Ray.
>
> On Sat, Aug 4, 2012 at 2:56 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>> Please install the current release version of R and edgeR.
>>
>> Gordon
>>
>>  Date: Thu,  2 Aug 2012 13:54:33 -0700 (PDT)
>>> From: "Surjyendu Ray [guest]" <guest at bioconductor.org>
>>> To: bioconductor at r-project.org, surjray at gmail.com
>>> Subject: [BioC] edgeR exactTest dispersion value of 0 gives error
>>>
>>>
>>> Dear all,
>>>
>>
>>          I am trying to see differentially expressed genes between two
>>> samples, each with three replicates. I am using edgeR to do the analysis.
>>> However, when I am running the exactTest using the following command, I am
>>> getting an error.
>>>
>>
>>  FM_HCV1_HCM1.exactTest2 = exactTest( FM_HCV1_HCM1.TagwiseDisp, pair = c(
>>> 1, 2 ), dispersion = 0 )
>>> The error message is:
>>> Error in binomTest(s1[pois], s2[pois], p = n1/(n1 + n2)) :
>>>  y1 and y2 must be non-negative
>>> If I do a traceback(), the output is:
>>> 4: stop("y1 and y2 must be non-negative")
>>> 3: binomTest(s1[pois], s2[pois], p = n1/(n1 + n2))
>>> 2: exactTestDoubleTail(y1, y2, dispersion = dispersion, big.count =
>>> big.count)
>>> 1: exactTest(FM_HCV1_HCM1.**TagwiseDisp, pair = c(1, 2), dispersion = 0)
>>>
>>>     However, any other value for dispersion is working well, especially
>>> values that are very small, e.g. 1e-10. I am confused as to why dispersion
>>> = 0 is producing that error.
>>>
>>
>>      Thanking you.
>>>
>>> -- output of sessionInfo():
>>>
>>> R version 2.14.1 (2011-12-22)
>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=C                 LC_NAME=C
>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] edgeR_2.4.6  limma_3.10.3

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