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

[Beth [guest]]

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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