[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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