[BioC] RPKM calculation genewise
Nicolas Delhomme
delhomme at embl.de
Wed Mar 6 16:54:02 CET 2013
Hi Amit,
I've Cc'ed the bioconductor mailing list as it might interest others.
Before I try to reproduce your error, can you please post your sessionInfo? I.e. the output of the sessionInfo() command executed in your R session once you've loaded easyRNASeq.
What analyses do you plan? I would personally not use RPKM for anything else than visualization.
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 Mar 6, 2013, at 4:13 PM, Amit Singh wrote:
>
> Hi,
>
> I am trying to use easyRNASeq package for the calculation of RPKM, but
> getting NA as normalized values for each genes.
>
> I am just testing with the test data provided by you. If it work, then i
> will use it for our analysis.
>
> rnaSeq1 <- easyRNASeq(system.file(
> "extdata",
> package="RnaSeqTutorial"),
> organism="Dmelanogaster",
> readLength=30L,
> annotationMethod="rda",
> annotationFile=system.file(
> "data",
> "gAnnot.rda",
> package="RnaSeqTutorial"),
> summarization="geneModels",
> count="genes",
> pattern="[A,C,T,G]{6}\\.bam$",
> outputFormat="RNAseq")
>
> feature.size = width(genomicAnnotation(rnaSeq1))
>
> head(readCounts(rnaSeq2,'genes','geneModels'))
> # here i am getting the counts
> ACACTG.bam ACTAGC.bam ATGGCT.bam TTGCGA.bam
> FBgn0000003 0 0 0 0
> FBgn0000008 0 0 1 0
> FBgn0000014 0 1 0 0
> FBgn0000015 0 0 0 0
> FBgn0000017 5 4 5 8
> FBgn0000018 0 1 1 0
>
> but on normalization (RPKM) , I am not getting normalized values
> head(RPKM(rnaSeq1,from="geneModels"))
> ACACTG.bam ACTAGC.bam ATGGCT.bam TTGCGA.bam
> FBgn0000003 NA NA NA NA
> FBgn0000008 NA NA NA NA
> FBgn0000014 NA NA NA NA
> FBgn0000015 NA NA NA NA
> FBgn0000017 NA NA NA NA
> FBgn0000018 NA NA NA NA
>
>
> Question :Could you please let me know, how can i get GENE WISE normalized
> values using easyRNASeq package?
>
>
> --
> Thanks & Regards,
>
> Amit Kumar Singh
> Project Engineer, Scientific & Engineering Computing Group
> National PARAM Supercomputing Facility,
> Centre for Development of Advanced Computing,
> Pune, MH -411007 , India
> Webportal: http://bioinfo-portal.cdac.in/
>
>
>
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