[BioC] Limma\'s roast() does not accept weigths in combination with block

Moritz Hess [guest] guest at bioconductor.org
Mon Aug 5 12:36:49 CEST 2013

Dear All,

I am conducting enrichment tests using Limma's roast() function.   As I am investigating RNA-Seq data, I have to introduce the weights calculated by voom(). Without a blocking variable, roast() runs without an itch but when I introduce a blocking variable (with or without correlation within blocks), roast() halts and returns "Can't use block with weights". Is the combination of weights and blocking variables in roast() generally impossible and if not, will it be possible in upcomming releases of limma?

Thank you very much in advance,


 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] DESeq_1.12.0       lattice_0.20-15    locfit_1.5-9.1     Biobase_2.20.0    
[5] BiocGenerics_0.6.0 statmod_1.4.17     edgeR_3.2.3        limma_3.16.5      

loaded via a namespace (and not attached):
 [1] annotate_1.38.0      AnnotationDbi_1.22.6 compiler_3.0.1      
 [4] DBI_0.2-7            genefilter_1.42.0    geneplotter_1.38.0  
 [7] grid_3.0.1           IRanges_1.18.1       RColorBrewer_1.0-5  
[10] RSQLite_0.11.4       stats4_3.0.1         survival_2.37-4     
[13] tools_3.0.1          XML_3.98-1.1         xtable_1.7-1  

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