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Last seen 9.6 years ago
Hi all,
I'm new to DESeq and am having a problem setting up the design matrix
for an experiment that has 3 biological conditions with 3 replicates
each and an additional factor to take into an experimental batch
effect.
I have proceeded in the following manner:
> library(DESeq)
> data <- read.table("aggregated_counts_final.txt", header=T,
row.names=1)
> condition <- c(rep("Control",3), rep("Rods",3), rep("Cubes",3))
> batch <- c(rep(c(1,2,3),3))
> Design <-
as.data.frame(cbind(condition,batch),row.names=colnames(data))
> CDS <- newCountDataSet(data,Design)
> CDS <- estimateSizeFactors(CDS)
> CDS <- estimateDispersions(CDS)
Error in .local(object, ...) :
None of your conditions is replicated. Use method='blind' to estimate
across conditions, or 'pooled-CR', if you have crossed factors.
I can't quite figure out where I've gone wrong... it seems specific to
my design matrix as this is very similar to the Pasilla data example,
but that works fine on my system. I suspect I'm not understanding
something very basic or there's some odd error.
Thanks so much,
Josh
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq_1.10.1 lattice_0.20-13 locfit_1.5-8 Biobase_2.18.0
BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] annotate_1.36.0 AnnotationDbi_1.20.3 DBI_0.2-5 genefilter_1.40.0
geneplotter_1.36.0 grid_2.15.2 IRanges_1.16.4 parallel_2.15.2
[9] RColorBrewer_1.0-5 RSQLite_0.11.2 splines_2.15.2 stats4_2.15.2
survival_2.37-2 tools_2.15.2 XML_3.95-0.1 xtable_1.7-0
--
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