[BioC] easyRNASeq error
Nicolas Delhomme
delhomme at embl.de
Fri Mar 2 15:37:04 CET 2012
Hi Wade,
Great! Thanks for the feedback!
Let me know for the other issue once you've got the time to try.
Cheers,
Nico
---------------------------------------------------------------
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 2 Mar 2012, at 15:33, Davis, Wade wrote:
> Hi Nico,
> Everything worked fine on your examples. Please see below for output.
>
> Thanks,
> Wade
>
>
> R Under development (unstable) (2012-02-28 r58513)
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> utils:::menuInstallLocal()
>> utils:::menuInstallLocal()
>> libary(easyRNASeq)
> Error: could not find function "libary"
>> library(easyRNASeq)
> Loading required package: parallel
> Loading required package: genomeIntervals
> Loading required package: intervals
> 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,
> intersect, lapply, Map, mapply, 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: biomaRt
> Loading required package: edgeR
> Loading required package: limma
> Loading required package: Biostrings
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:intervals':
>
> reduce
>
>
> Attaching package: 'Biostrings'
>
> The following object(s) are masked from 'package:intervals':
>
> type
>
> Loading required package: BSgenome
> Loading required package: GenomicRanges
>
> Attaching package: 'GenomicRanges'
>
> The following object(s) are masked from 'package:genomeIntervals':
>
> strand, strand<-
>
> Loading required package: DESeq
> Loading required package: locfit
> Loading required package: akima
> Loading required package: lattice
> locfit 1.5-6 2010-01-20
> Loading required package: Rsamtools
> Loading required package: ShortRead
> Loading required package: latticeExtra
> Loading required package: RColorBrewer
>
> Attaching package: 'ShortRead'
>
> The following object(s) are masked from 'package:locfit':
>
> left, right
>
> Warning messages:
> 1: replacing previous import 'coerce' when loading 'intervals'
> 2: replacing previous import 'initialize' when loading 'intervals'
>> sessionInfo()
> R Under development (unstable) (2012-02-28 r58513)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] easyRNASeq_1.1.8 ShortRead_1.13.13 latticeExtra_0.6-20 RColorBrewer_1.0-5
> [5] Rsamtools_1.7.37 DESeq_1.7.6 locfit_1.5-6 lattice_0.20-0
> [9] akima_0.5-7 BSgenome_1.23.2 GenomicRanges_1.7.28 Biostrings_2.23.6
> [13] IRanges_1.13.26 edgeR_2.5.9 limma_3.11.15 biomaRt_2.11.1
> [17] Biobase_2.15.3 BiocGenerics_0.1.7 genomeIntervals_1.11.0 intervals_0.13.3
>
> loaded via a namespace (and not attached):
> [1] annotate_1.33.2 AnnotationDbi_1.17.22 bitops_1.0-4.1 DBI_0.2-5 genefilter_1.37.0
> [6] geneplotter_1.33.1 grid_2.15.0 hwriter_1.3 RCurl_1.91-1.1 RSQLite_0.11.1
> [11] splines_2.15.0 survival_2.36-12 tools_2.15.0 XML_3.9-4.1 xtable_1.7-0
> [16] zlibbioc_1.1.1
>> library("easyRNASeq")
>> library("RnaSeqTutorial")
>> library(BSgenome.Dmelanogaster.UCSC.dm3)
>>
>> rnaSeq <- easyRNASeq(system.file(
> + "extdata",
> + package="RnaSeqTutorial"),
> + organism="Dmelanogaster",
> + chr.sizes=as.list(seqlengths(Dmelanogaster)),
> + readLength=36L,
> + annotationMethod="rda",
> + annotationFile=system.file(
> + "data",
> + "gAnnot.rda",
> + package="RnaSeqTutorial"),
> + format="bam",
> + count="genes",
> + summarization="geneModels",
> + pattern="[A,C,T,G]{6}\\.bam$",
> + outputFormat="RNAseq")
> Checking arguments...
> Fetching annotations...
> Computing gene models...
> Summarizing counts...
> Processing ACACTG.bam
> Processing ACTAGC.bam
> Processing ATGGCT.bam
> Processing TTGCGA.bam
> Preparing output
> Warning message:
> In easyRNASeq(system.file("extdata", package = "RnaSeqTutorial"), :
> There are 2238 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
>> rnaSeqPar <- easyRNASeq(system.file(
> + "extdata",
> + package="RnaSeqTutorial"),
> + organism="Dmelanogaster",
> + chr.sizes=as.list(seqlengths(Dmelanogaster)),
> + readLength=36L,
> + annotationMethod="rda",
> + annotationFile=system.file(
> + "data",
> + "gAnnot.rda",
> + package="RnaSeqTutorial"),
> + format="bam",
> + count="genes",
> + summarization="geneModels",
> + pattern="[A,C,T,G]{6}\\.bam$",
> + outputFormat="RNAseq",
> + nbCore=2)
> Checking arguments...
> Fetching annotations...
> Computing gene models...
> Summarizing counts...
> Processing ACACTG.bam
> Processing ACTAGC.bam
> Processing ATGGCT.bam
> Processing TTGCGA.bam
> Preparing output
> Warning message:
> In easyRNASeq(system.file("extdata", package = "RnaSeqTutorial"), :
> There are 2238 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
>>
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