Hi Alejandro,
I am analyzing with DEXSeq my data. 4 CTRLs and 2 Treated samples. My
design is the following:

design(ecs.24)

      sampleName                                 fileName condition
experiment

H1            H1    Exon_Martelli_Sample_Martelli_H_1.bam   HYPOXIA
RUN_2

H2            H2    Exon_Martelli_Sample_Martelli_H_2.bam   HYPOXIA
RUN_2

N1            N1    Exon_Martelli_Sample_Martelli_N_1.bam      CTRL
RUN_2

N2            N2    Exon_Martelli_Sample_Martelli_N_2.bam      CTRL
RUN_2

CTRL2      CTRL2 Exon_Martelli_Sample_Martelli_CTRL_2.bam      CTRL
RUN_1

CTRL3      CTRL3 Exon_Martelli_Sample_Martelli_CTRL_3.bam      CTRL
RUN_1

When I follow the vignette:

ecs.24 <- estimateDispersions(ecs.24,nCores=8)

....Done

ecs.24 <- fitDispersionFunction(ecs.24)

....Done

ecs.24 <- testForDEU(ecs.24, nCores=8)

.....

ecs.24 <- estimatelog2FoldChanges(ecs.24, nCores=8)

*Error in `row.names<-.data.frame`(`*tmp*`, value = c("geneID", "exonID",
: *

*  duplicate 'row.names' are not allowed*

*Calls: estimatelog2FoldChanges ... pData<- -> pData<- -> row.names<- ->
row.names<-.data.frame*

*In addition: Warning message:*

*non-unique value when setting 'row.names': 'log2fold(CTRL/HYPOXIA)' *


I checked for duplication as you had suggested elsewhere

any(duplicated(featureNames(ecs.24)))

[1] FALSE

 any(duplicated(paste(geneIDs(ecs.24),exonIDs(ecs.24),sep=":")))

[1] FALSE


I also checked that the condition in design where factors:


is.factor(pData(ecs.24)$condition)

[1] TRUE


The only explanation I could come to is the fact that I have an even number
of samples for control and treated? or that I have the 'experiment' column
in the design, but it would be irrelevant since the default formula is only
taking condition into consideration, isn't it?

What could be the origin of the error?

Thanks again!

Jose



> sessionInfo()

R version 3.0.1 (2013-05-16)

Platform: x86_64-unknown-linux-gnu (64-bit)


locale:

 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US

 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US

 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C

[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C


attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods

[8] base


other attached packages:

[1] DEXSeq_1.8.0       Biobase_2.22.0     BiocGenerics_0.8.0


loaded via a namespace (and not attached):

 [1] biomaRt_2.18.0       Biostrings_2.30.1    bitops_1.0-6

 [4] GenomicRanges_1.14.3 hwriter_1.3          IRanges_1.20.6

 [7] RCurl_1.95-4.1       Rsamtools_1.14.2     statmod_1.4.18

[10] stats4_3.0.1         stringr_0.6.2        tools_3.0.1

[13] XML_3.98-1.1         XVector_0.2.0        zlibbioc_1.8.0


2014-03-13 16:32 GMT+01:00 Alejandro Reyes <alejandro.reyes@embl.de>:

> Dear Xiayu Rao,
>
> Thanks for your interest in DEXSeq.
> That looks strange, does it happen when you use files different from the
> one you generated by your own? Could you maybe send me (offline) your
> gtf file and the first 1000 lines of one of your sam files?
>
> Bests,
> Alejandro
>
> > Hello,
> >
> > DEXSeq is a great tool. Thank you for that. I recently generate my own
> gtf file with the same format as the exon.gff generated by
> dexseq_prepare_annotation.py. However, the output is strange. I tried to
> find the reason with no success. Could you please provide any idea about
> that problem? Thank you very much in advance!
> >
> > Note: I used the latest dexseq, and the sam files had been sorted.
> >
> > 1       genes.gtf       exonic_part     12228   12594   .       +
> .       exonic_part_number "001"; gene_id "ENSG00000223972"
> > 1       genes.gtf       exonic_part     12722   12974   .       +
> .       exonic_part_number "002"; gene_id "ENSG00000223972"
> > 1       genes.gtf       exonic_part     13053   13220   .       +
> .       exonic_part_number "003"; gene_id "ENSG00000223972"
> > 1       genes.gtf       exonic_part     14830   14969   .       -
> .       exonic_part_number "001"; gene_id "ENSG00000223972+ENSG00000227232"
> > .............
> >
> >
> > ==> SRR791043_counts.txt <==
> > :001G00027000003"
> > :002G00021000003"
> > :003G00070000003"
> > :004G00040000003"
> > :005G00060000003"
> > :006G00030000003"
> > :007G00019000003"
> > :008G00045600003"
> > :009G00020400003"
> > :001G00000000005"
> >
> >
> > Thanks,
> > Xiayu
>
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-- 
Jose M. Garcia Manteiga PhD
Research Assistant - Data Analysis in Functional Genomics
Center for Translational Genomics and BioInformatics
Dibit2-Basilica, 3A3
San Raffaele Scientific Institute
Via Olgettina 58, 20132 Milano (MI), Italy

Tel: +39-02-2643-4751
e-mail: garciamanteiga.josemanuel@hsr.it

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