Because you only have one exon that is expressed by the samples, the two exons can't be tested for different proportions of usage.
---- Original message ---- >Date: Wed, 17 Aug 2011 17:12:03 +0200 >From: bioc-sig-sequencing-boun...@r-project.org (on behalf of Jane Merlevede ><jane.merlev...@gmail.com>) >Subject: Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons >To: bioc-sig-sequencing@r-project.org > >Dear Wolfgang, dear Simon, > >Thanks for the explanation, I did not have understand well the purpose >of DEXSeq. >If you are interested, here are the cases in my dataset where genes >have more than 1 exon, but testGeneForDEU did not give a result: > >*The simplest case:* >res1[1449:1451,] > geneID exonID dispersion_CR_est dispersion pvalue >EHI_031280:001 EHI_031280 E001 0.25177357 2.517736e-01 0.837492 >EHI_031280:002 EHI_031280 E002 0.03580064 3.580064e-02 0.837492 >EHI_031280:003 EHI_031280 E003 NA 1.000000e+08 NA > padjust >EHI_031280:001 0.9746982 >EHI_031280:002 0.9746982 >EHI_031280:003 NA > >And the read counts per exon are: >exon_counts[1449:1451,] > exon_ID FKKM1_1 FPKM1_2 FPKM1_3 FPKM2_1 FPKM2_2 FPKM2_3 >1449 EHI_031280:001 9 9 5 33 7 2 >1450 EHI_031280:002 155 192 220 453 133 176 >1451 EHI_031280:003 0 0 0 0 0 0 > >One exon in the gene has 0 for all FPKM => 10^8 dispersion and no >result for the test. I am not surprised, contrary to *this second >case*: > res1[1227:1228,] > geneID exonID dispersion_CR_est dispersion pvalue padjust >EHI_025270:001 EHI_025270 E001 NA 1.00000e+08 NA NA >EHI_025270:002 EHI_025270 E002 NA 2.03465e-02 NA NA > >And the read counts per exon are: > exon_counts[1227:1228,] > exon_ID FKKM1_1 FPKM1_2 FPKM1_3 FPKM2_1 FPKM2_2 FPKM2_3 >1227 EHI_025270:001 0 0 0 0 0 0 >1228 EHI_025270:002 11900 3012 12136 10971 7387 5923 > >Why is there no result for the second exon? > >Thanks, >Jane > > >"Dear Jane, > >in the case of genes (or better term: loci) with only one exon, DEXSeq's >testGeneForDEU does not make sense - it is looking for exons within the >locus that behave differently from the average of all the others: there >are no others! Hence the parameters are unidentifiable, and the software >should not even look at them. We'll robustify the software for this case >in future versions (note that the package is still actively being >developed). > >The case of the NA values that are not explained by there only being one >exon is more interesting. Can you send us the code to reproduce your >problem (this also requires the data, which you can send offline, and in >which you can for instance anonymize the gene and sample annotations). > > Best wishes > Wolfgang > >Hi Jane > >On 08/08/2011 02:45 PM, Wolfgang Huber wrote: >>* in the case of genes (or better term: loci) with only one exon, DEXSeq's >*>* testGeneForDEU does not make sense - it is looking for exons within the >*>* locus that behave differently from the average of all the others: there >*>* are no others! Hence the parameters are unidentifiable, and the software >*>* should not even look at them. >* >Actually, it doesn't. This is why the p value is NA. Also note the >column 'testable' in the fData data frame: it is set to FALSE in such >cases to indicate that a test was not attempted. You will also find >testable=FALSE occasionally in genes with more than one exons, namely >whenever all exons or all exons but one have zero counts in all samples. > >Cheers > Simon" > > > >2011/7/29 Jane Merlevede <jane.merlev...@gmail.com> > >> Hello, >> >> I am using DEXseq for differential analysis. I have posted some e-mails >> about it already on this list, but I have more questions ! >> My dataset has 2 conditions with 3 biological replicates per condition: >> >> pData(ecs) >> sizeFactor condition replicate type >> Raman_1 0.9638822 nonvir 1 paired-end >> HM1_1 1.4000715 vir 1 paired-end >> Raman_2 1.0314049 nonvir 2 paired-end >> Raman_3 1.0734133 nonvir 3 paired-end >> HM1_2 0.7801269 vir 2 paired-end >> HM1_3 0.9488409 vir 3 paired-end >> >> >> I found the number of differentially expressed exons. I would like to know >> also which are down and which are up regulated. This information is given by >> foldChange, which is not provided in DEXSeq (res1). >> >> res1 <- DEUresultTable(ecs) >> head(res1) >> geneID exonID dispersion_CR_est dispersion pvalue >> EHI_000010:001 EHI_000010 E001 NA 0.02377712 NA >> EHI_000130:001 EHI_000130 E001 0.07466945 0.07466945 0.4867354 >> EHI_000130:002 EHI_000130 E002 0.12897281 0.12897281 0.9427953 >> EHI_000130:003 EHI_000130 E003 0.01960222 0.02031871 0.8432791 >> EHI_000130:004 EHI_000130 E004 0.06733720 0.06733720 0.7042977 >> EHI_000240:001 EHI_000240 E001 0.04375400 0.04375400 0.7493987 >> padjust >> EHI_000010:001 NA >> EHI_000130:001 0.8639624 >> EHI_000130:002 0.9927663 >> EHI_000130:003 0.9756197 >> EHI_000130:004 0.9503086 >> EHI_000240:001 0.9611397 >> >> So I would like to know, if it could be possible to have baseMean, >> baseMeanA, baseMeanB, foldChange, log2FoldCHange, resVarA and resVarB as in >> DESeq? >> >> Since this does not seem to be implemented in DEXSeq, I should start with >> the read counts per exon table to get it, but I can't find it neither. I >> think it is use in the estimateSizeFactors function, but I don't manage to >> access it. It's a pity, I will have to reconstruct the table... >> >> >> Thank you for your help, >> Jane Merlev�de >> > > [[alternative HTML version deleted]] > >________________ >_______________________________________________ >Bioc-sig-sequencing mailing list >Bioc-sig-sequencing@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing