R version 2.15.2 (2012-10-26) -- "Trick or Treat"
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ISBN 3-900051-07-0
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> library("pasilla")
Loading required package: DEXSeq
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
> inDir = system.file("extdata", package="pasilla", mustWork=TRUE)
> dir(inDir)
 [1] "Dmel.BDGP5.25.62.DEXSeq.chr.gff" "geneIDsinsubset.txt"            
 [3] "pasilla_gene_counts.tsv"         "treated1fb.txt"                 
 [5] "treated2fb.txt"                  "treated3fb.txt"                 
 [7] "untreated1fb.txt"                "untreated2fb.txt"               
 [9] "untreated3fb.txt"                "untreated4fb.txt"               
> 
> setwd("/home/korlin/Temp")
> samples<-read.table('fly', header=T, sep="\t")
> rownames(samples)<-samples[,1]
> samples[,1] <- NULL
> print(samples)
             condition       type
treated1fb     treated paired-end
treated2fb     treated paired-end
treated3fb     treated paired-end
untreated1fb untreated paired-end
untreated2fb untreated paired-end
untreated3fb untreated paired-end
untreated4fb untreated paired-end
> #print(rownames(samples))
> annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")
> library("DEXSeq")
> ecs = read.HTSeqCounts(countfiles = file.path(inDir, paste(rownames(samples), "txt", sep=".")),design = samples,flattenedfile = annotationfile)
> sampleNames(ecs) = rownames(samples)
> genesforsubset = readLines(file.path(inDir, "geneIDsinsubset.txt"))
> pasillaExons = subsetByGenes(ecs, genes=genesforsubset)
> library("DESeq")
> genetable = geneCountTable(ecs)
> pasillaGenes = newCountDataSet(genetable,conditions = samples)
> save(pasillaExons, file=file.path("/home/korlin/Temp/R-2.15.2/library/pasilla/data", "pasillaExons.RData"))
> save(pasillaGenes, file=file.path("/home/korlin/Temp/R-2.15.2/library/pasilla/data", "pasillaGenes.RData"))
> toLatex(sessionInfo())
\begin{itemize}\raggedright
  \item R version 2.15.2 (2012-10-26), \verb|x86_64-unknown-linux-gnu|
  \item Locale: \verb|LC_CTYPE=en_US.UTF-8|, \verb|LC_NUMERIC=C|, \verb|LC_TIME=en_US.UTF-8|, \verb|LC_COLLATE=en_US.UTF-8|, \verb|LC_MONETARY=en_US.UTF-8|, \verb|LC_MESSAGES=en_US.UTF-8|, \verb|LC_PAPER=C|, \verb|LC_NAME=C|, \verb|LC_ADDRESS=C|, \verb|LC_TELEPHONE=C|, \verb|LC_MEASUREMENT=en_US.UTF-8|, \verb|LC_IDENTIFICATION=C|
  \item Base packages: base, datasets, graphics, grDevices, methods,
    stats, utils
  \item Other packages: Biobase~2.18.0, BiocGenerics~0.4.0,
    DESeq~1.10.1, DEXSeq~1.4.0, lattice~0.20-29, locfit~1.5-9.1,
    pasilla~0.2.15
  \item Loaded via a namespace (and not attached): annotate~1.36.0,
    AnnotationDbi~1.20.7, biomaRt~2.14.0, DBI~0.2-7, genefilter~1.40.0,
    geneplotter~1.36.0, grid~2.15.2, hwriter~1.3, IRanges~1.16.6,
    parallel~2.15.2, RColorBrewer~1.0-5, RCurl~1.95-4.1,
    RSQLite~0.11.4, splines~2.15.2, statmod~1.4.19, stats4~2.15.2,
    stringr~0.6.2, survival~2.37-7, XML~3.98-1.1, xtable~1.7-3
\end{itemize}
> 	
> data("pasillaExons", package="pasilla")
> pasillaExons <- makeCompleteDEUAnalysis(pasillaExons,formulaDispersion=count ~ sample + condition*exon,minCount=0, maxExon=100, formula0=NULL, formula1=NULL, FDR=0.05, fitExpToVar="condition", nCores=1, path=NULL, color=NULL, color.samples=NULL, quiet=FALSE)
Error in fitDispersionFunction(ecs) : 
  no CR dispersion estimations found, please first call estimateDispersions function
Calls: makeCompleteDEUAnalysis -> fitDispersionFunction
In addition: Warning message:
In .local(object, ...) :
  Failed to set up model frames for genes  FBgn0000256, FBgn0000578, FBgn0002921, FBgn0003089, FBgn0010226, FBgn0010280, FBgn0010638, FBgn0010808, FBgn0010909, FBgn0011300, FBgn0013811, FBgn0015278, FBgn0020309, FBgn0020372, FBgn0026777, FBgn0027084, FBgn0027579, FBgn0028341, FBgn0030170, FBgn0030302, FBgn0031108, FBgn0032003, FBgn0032785, FBgn0032979, FBgn0034158, FBgn0034180, FBgn0034420, FBgn0037050, FBgn0037683, FBgn0037926, FBgn0038725, FBgn0039776, FBgn0039914, FBgn0040297, FBgn0050460, FBgn0051021, FBgn0051352, FBgn0051790, FBgn0051847, FBgn0085442, FBgn0250871, FBgn0259735, FBgn0261573
Execution halted