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,exonExonI ntervals,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 [[alternative HTML version deleted]]

Try replacing your "I(exon==exonID)" with "exon" for TRT. The default formula1 for testForDEUTRT shows why this might work, and is also different from default formula1 for testForDEU. > args(testForDEUTRT) function (ecs, nCores = 1, formula0 = ~sample + condition + exon, formula1 = ~sample + condition * exon, dispColumn = "dispersion") The formula applies to the following data frame, and might give you some more insight. See also here if you haven't already: https://stat.ethz.ch/pipermail/bioconductor/2013-January/050253.html > data(pasillaExons, package="pasilla") > modelFrameForTRT(pasillaExons) sample condition type sizeFactor exon 1 treated1fb treated single-read NA this 2 treated2fb treated paired-end NA this 3 treated3fb treated paired-end NA this 4 untreated1fb untreated single-read NA this 5 untreated2fb untreated single-read NA this 6 untreated3fb untreated paired-end NA this 7 untreated4fb untreated paired-end NA this 8 treated1fb treated single-read NA others 9 treated2fb treated paired-end NA others 10 treated3fb treated paired-end NA others 11 untreated1fb untreated single-read NA others 12 untreated2fb untreated single-read NA others 13 untreated3fb untreated paired-end NA others 14 untreated4fb untreated paired-end NA others ~Mani -----Original Message----- From: Christopher DeBoever [mailto:cdeboeve@ucsd.edu] Sent: Monday, May 20, 2013 3:57 PM To: bioconductor at r-project.org Subject: [BioC] DEXSeq: formulas for testForDEUTRT 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,exonExonI ntervals,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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor