Hi Gordon,

thanks for your response. I appreciate very much to hear that this feature
will be implemented in future releases of limma.

Best regards,

Moritz

2013/8/6 Gordon K Smyth <smyth@wehi.edu.au>

>  Date: Mon,  5 Aug 2013 03:36:49 -0700 (PDT)
>> From: "Moritz Hess [guest]" <guest@bioconductor.org>
>> To: bioconductor@r-project.org, ssehztirom@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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