[BioC] Question about decideTestsDGE

Gordon K Smyth smyth at wehi.EDU.AU
Fri Aug 1 02:40:52 CEST 2014


Dear Jon,

No, you can't use decideTestsDGE() to count the number of DE genes when 
doing a test for multiple contrasts at once.  The whole purpose of 
decideTestDGE is to count up and down regulated genes.  However when you 
are doing a test for multiple coefficients or contrasts, then the test is 
analogous to an F-test on more than one degree of freedom.  There is no 
concept of directionality for an F-test, i.e., you can't classify a 
significant result as being up or down, just not all zero.

The same situation exists for the corresponding function in limma. 
decideTests() can be used for t-tests but not for F-tests.

Best wishes
Gordon



> Date: Thu, 31 Jul 2014 09:50:51 +0000
> From: Jon Brate <jon.brate at ibv.uio.no>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] Question about decideTestsDGE()
>
> Hi,
>
> In edgeR I performed LRT for all groups against the reference like this:
>
>> lrtAll = glmLRT(fit, coef=2:10)
>
> I wonder if it is possible to use decideTestsDGE() to find out the 
> number of upregulated DE genes? I can use it when I perform LRT to 
> compare one group against the reference but on lrtAll I get the error 
> message:
>
>> decideTestsDGE(lrtAll)
> Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  :
>  'data' must be of a vector type, was 'NULL'
>
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] edgeR_3.6.4  limma_3.20.8
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.26.0    Biobase_2.24.0          BiocGenerics_0.10.0     DBI_0.2-7
> [5] DESeq2_1.4.5            GenomeInfoDb_1.0.2      GenomicRanges_1.16.3    IRanges_1.22.9
> [9] RColorBrewer_1.0-5      RSQLite_0.11.4          Rcpp_0.11.2             RcppArmadillo_0.4.320.0
> [13] XML_3.98-1.1            XVector_0.4.0           annotate_1.42.0         genefilter_1.46.1
> [17] geneplotter_1.42.0      grid_3.1.0              lattice_0.20-29         locfit_1.5-9.1
> [21] parallel_3.1.0          stats4_3.1.0            survival_2.37-7         tools_3.1.0
> [25] xtable_1.7-3
>
>
> ----------------------------------------------------------------
> Jon Bråte
>
> Section for Genetics and Evolutionary Biology (EVOGENE)
> Department of Biosciences
> University of Oslo
> P.B. 1066 Blindern
> N-0316, Norway
> Email: jon.brate at ibv.uio.no<mailto:jon.brate at ibv.uio.no>
> Phone: 922 44 582
> Web: mn.uio.no/ibv/english/people/aca/jonbra/index.html<http://mn.uio.no/ibv/english/people/aca/jonbra/index.html>

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