Question: Limma\'s roast() does not accept weigths in combination with block
6.2 years ago by
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Guest User • 12k wrote:
Dear All, I am conducting enrichment tests using Limma's roast() function. As I am investigating RNA-Seq data, I have to introduce the weights calculated by voom(). Without a blocking variable, roast() runs without an itch but when I introduce a blocking variable (with or without correlation within blocks), roast() halts and returns "Can't use block with weights". Is the combination of weights and blocking variables in roast() generally impossible and if not, will it be possible in upcomming releases of limma? Thank you very much in advance, Moritz -- output of sessionInfo(): sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C  LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8  LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel splines stats graphics grDevices utils datasets  methods base other attached packages:  DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0  BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 loaded via a namespace (and not attached):  annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1  DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0  grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5  RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4  tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
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