[BioC] edgeR: dispersion estimation

[Yanzhu [guest]]

Dear Gordon,

Sorry for replying late, I am sick and take some days off. The following are my answers to your questions:

I have checked they are all integers, they are read counts generated by HT-Seq (v0.5.3p9). When I type your command I get zero as below:

max(y$counts-floor(y$counts))
[1] 0


I have also posted the session information as below. Both the R and edgeR package are the most recent versions. However, the results are still the same as before. 

Are there other possible reasons that would cause such issue?


Thank you very much for your help! I greatly appreciate it.



Yanzhu


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Dear Yanzhu,

I find it hard to believe that your data are all integers, because there 
is something seriously wrong, and we have only ever seen the problem you 
report when there are fractional counts.

How have you checked that they are all integers?  How were the counts 
created?  What do you see if you type:

   max(y$counts-floor(y$counts))

It also isn't clear that you have installed the current version of edgeR. 
Have you installed R 3.1.0?  Can you please give the sessionInfo() output? 
The current version of edgeR is 3.6.1, whereas you seem to be using 
version 3.2.4, which is two Bioconductor releases out of date.

Gordon



 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

other attached packages:
[1] DESeq_1.16.0         lattice_0.20-29      locfit_1.5-9.1       Biobase_2.24.0       BiocGenerics_0.10.0 
[6] edgeR_3.6.1          limma_3.20.1         BiocInstaller_1.14.2

loaded via a namespace (and not attached):
 [1] annotate_1.42.0      AnnotationDbi_1.26.0 DBI_0.2-7            genefilter_1.46.0    geneplotter_1.42.0  
 [6] GenomeInfoDb_1.0.2   grid_3.1.0           IRanges_1.22.6       RColorBrewer_1.0-5   RSQLite_0.11.4      
[11] splines_3.1.0        stats4_3.1.0         survival_2.37-7      tools_3.1.0          XML_3.98-1.1        
[16] xtable_1.7-3        
> 

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