I am working on some microarray data where the samples come from patients with different severities of disease state - something like "mild", "moderate", "severe". I suppose this is an 'ordinal' variable, but only know how to input categorical and continuous variables into the model and searching the Limma manual for the word 'ordinal' doesn't get me anywhere. Is it possible to work ordinal variables into my model? If not and I still want to use Limma is it best to treat it as categorical or continuous? Or is there an alternative package I could use which has this functionality? Many thanks in advance, Scott -- 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 Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] limma_3.16.7 sparcl_1.0.3 lattice_0.20-23 [4] corrplot_0.71 affyPLM_1.36.0 preprocessCore_1.22.0 [7] simpleaffy_2.36.1 gcrma_2.32.0 genefilter_1.42.0 [10] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 annotate_1.38.0 AnnotationDbi_1.22.6 [4] BiocInstaller_1.10.3 Biostrings_2.28.0 DBI_0.2-7 [7] grid_3.0.1 IRanges_1.18.3 RSQLite_0.11.4 [10] splines_3.0.1 stats4_3.0.1 survival_2.37-4 [13] XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.