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/ > > > > -------------------------------------------------------------------- ----------------------------------------------------------- > > This e-mail is for the sole use of the intended recipient(s) and may > contain confidential and privileged information. If you are not the > intended recipient, please contact the sender by reply e-mail and destroy > all copies and the original message. Any unauthorized review, use, > disclosure, dissemination, forwarding, printing or copying of this email > is strictly prohibited and appropriate legal action will be taken. > -------------------------------------------------------------------- ----------------------------------------------------------- >