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

[Gordon K Smyth]

> Date: Mon,  5 Aug 2013 03:36:49 -0700 (PDT)
> From: "Moritz Hess [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, ssehztirom at gmail.com
> Subject: [BioC] Limma\'s roast() does not accept weigths in
> 	combination with	block
>
> 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

Not impossible, but requires some careful special case programming.

> and if not, will it be possible in upcomming releases of limma?

Yes, but not in the next few weeks.

Gordon

> Thank you very much in advance,
>
> Moritz
>
> -- output of sessionInfo():
>
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
> [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=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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