[BioC] edgeR exactTest dispersion value of 0 gives error

Surjyendu Ray [guest] guest at bioconductor.org
Thu Aug 2 22:54:33 CEST 2012

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)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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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