Hi,

I run the example of read.HTSeqCounts() from DEXSeq, get following Error:

Error: all(unlist(lapply(design, class)) == "factor") is not TRUE

Any suggestion?  Thanks in advance.

Regards,
Sheng


code:

library(DEXSeq)
inDir = system.file("extdata", package="pasilla", mustWork=TRUE)
annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")
samples = data.frame(
condition = c(rep("treated", 3), rep("untreated", 4)),
replicate = c(1:3, 1:4),
row.names = dir(system.file("extdata", package="pasilla", mustWork=TRUE),
pattern="fb.txt"),
stringsAsFactors = TRUE,
check.names = FALSE
)

annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")


ecs = read.HTSeqCounts(countfiles = file.path(inDir, rownames(samples)),
design = samples,
flattenedfile = annotationfile)


sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] DEXSeq_1.3.16      Biobase_2.17.6     BiocGenerics_0.3.1

loaded via a namespace (and not attached):
[1] RCurl_1.91-1   XML_3.9-4      biomaRt_2.13.2 hwriter_1.3    plyr_1.7.1
    statmod_1.4.15 stringr_0.6.1

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