[BioC] edgeR exactTest dispersion value of 0 gives error

[Gordon K Smyth]

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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