[BioC] Limma\'s roast() does not accept weigths in combination with block
Gordon K Smyth
smyth at wehi.EDU.AU
Tue Aug 6 13:17:28 CEST 2013
> 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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