Hi all,

I'm trying to use DEXSeq's testForDEUTRT and provide my own model formulas
but I am running into an error:

Error in unique(c("AsIs", oldClass(x))) : object 'exonID' not found

I have used similar formulas for testForDEU in the past, so I'm not sure
why this isn't working. Has anyone been able to provide formulas to
testForDEUTRT? I've provided my commands below.

code:

library(DEXSeq)
library(multicore)

# read files
...

exonECS =
newExonCountSet(exonCountData,design,exonGeneIDs,exonExonIDs,exonExonIntervals,exonTranscripts)
exonECS <- estimateSizeFactors(exonECS)
formuladispersion = ~ sample + (exon + condition) * group
exonECS <-
estimateDispersionsTRT(exonECS,formula=formuladispersion,nCores=28)
exonECS <- fitDispersionFunction(exonECS)

formula0 = ~ sample + condition * exon + group
formula1 = ~ sample + condition * exon + group * I(exon == exonID)

exonECS <- testForDEUTRT(exonECS,formula0 = formula0,formula1 =
formula1,nCores=28)




> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] multicore_0.1-7    DEXSeq_1.6.0       Biobase_2.20.0
BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0       Biostrings_2.28.0    bitops_1.0-5
 [4] GenomicRanges_1.12.2 hwriter_1.3          IRanges_1.18.0
 [7] RCurl_1.95-4.1       Rsamtools_1.12.2     statmod_1.4.17
[10] stats4_3.0.0         stringr_0.6.2        XML_3.96-1.1
[13] zlibbioc_1.6.0



Thank you,

Chris DeBoever

Frazer Laboratory
Bioinformatics and Systems Biology
University of California San Diego

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