[BioC] RPKM calculation genewise

[Nicolas Delhomme]

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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