[BioC] Power Calculation of multiple factors design of RNA-sequencing study

[Yanzhu [guest]]

Dear Community,

I am working on the power calculation of a multiple factors design of RNA-Sequencing study. My project has three factors, I use generalized linear model to fit the model including three main effects, two-way interaction terms and the three-way interaction term. The model fitting is implemented by using DESeq and edgeR package. We would like to see how much power we have for this design. My question is:
Can the power calculation function provided in RNASeqPower R package fit in our setup? Since we have three factors instead of only compare two conditions.


Thanks,


Yanzhu   

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
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 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] RColorBrewer_1.0-5 DESeq_1.12.1       lattice_0.20-15    locfit_1.5-9.1     Biobase_2.20.1     BiocGenerics_0.6.0 edgeR_3.2.4        limma_3.16.8      

loaded via a namespace (and not attached):
 [1] annotate_1.38.0      AnnotationDbi_1.22.6 DBI_0.2-7            genefilter_1.42.0    geneplotter_1.38.0   grid_3.0.1           IRanges_1.18.4       RSQLite_0.11.4      
 [9] splines_3.0.1        stats4_3.0.1         survival_2.37-4      tools_3.0.1          XML_3.98-1.1         xtable_1.7-1        
> 


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