[BioC] EdgeR multi-factors testing questions

[Ryan C. Thompson]

I don't think it's surprising. TMM and upper quartile tend to give very 
similar normalization factors. Are you getting *exactly* identical 
P-values, or only very similar ones? Also, you can check the 
normalization factors themselves to see how much of a difference there 
is. If "d" is your DGEList object, you can get the normalization 
factors by typeing "d$samples$norm.factors.

-Ryan

On Mon 27 Jan 2014 05:16:13 AM PST, Yanzhu [guest] wrote:
>
> Hi Gordon,
>
> I have one more question about edgeR. I have used different normalization methods to normalize the data and then test the main effects, the two-way interaction terms and the three-way interaction term as we discussed before. To my surprise, the P-values results of the testings are the same for data normalized by TMM and Upper quartile. Is it possible?
>
>
> Best,
>
>
> Yanzhu
>
>
> ---------------------------------------------------------
>
>
> Dear Yanzhu,
>
> Yes, that's how I would do it.  Keep the same dispersions for all fits.
>
> Best wishes
> Gordon
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> 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] DESeq_1.12.1       lattice_0.20-15    locfit_1.5-9.1     Biobase_2.20.1     BiocGenerics_0.6.0
> [6] edgeR_3.2.4        limma_3.16.8
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.38.0      AnnotationDbi_1.22.6 DBI_0.2-7            genefilter_1.42.0
>   [5] geneplotter_1.38.0   grid_3.0.1           IRanges_1.18.4       RColorBrewer_1.0-5
>   [9] RSQLite_0.11.4       splines_3.0.1        stats4_3.0.1         survival_2.37-4
> [13] tools_3.0.1          XML_3.98-1.1         xtable_1.7-1
>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor