[BioC] limma -roast: probe-level vs gene-level?

[Gordon K Smyth]

Dear Beth,

You can include all probes for all genes in a given pathway.  That's what 
I do.

It would not be wrong to choose one good probe for each gene (if chosen 
independently of differential expression), but including multiple probes 
when they are available gives more power.

Best wishes
Gordon

> Date: Thu,  8 May 2014 10:50:16 -0700 (PDT)
> From: "Beth [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, wilmotb at ohsu.edu
> Subject: [BioC] limma -roast:  probe-level vs gene-level?
>
> Hi,

> What is the best way to use roast for platforms where there are multiple 
> probes per gene? Is it best to choose one probe per gene or for 
> instance, should all probes in all the genes in a given pathway be 
> entered?

> Thanks,
> Beth
>
> -- output of sessionInfo():
>
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
> [3] 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] biomaRt_2.20.0       IRanges_1.22.6       BiocGenerics_0.10.0  BiocInstaller_1.14.2
> [5] edgeR_3.6.1          limma_3.20.1
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.26.0 Biobase_2.24.0       DBI_0.2-7            GenomeInfoDb_1.0.2
> [5] RCurl_1.95-4.1       RSQLite_0.11.4       stats4_3.1.0         tools_3.1.0
> [9] XML_3.98-1.1

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