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@ibv.uio.no<mailto:jon.brate@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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