Hello,

I have been trying to use DEXSeq to do a DEU analysis and plot some of the genes that are coming up in the results. The analysis seems to be working fine (even though I am getting a warning when I estimate the dispersion) and I have about 2000 hits, but when I try to visualise the differences using the plot I get this error:

 plotDEXSeq(dxr1, "ENSG00000163660", displayTranscripts=T,legend=TRUE,  cex.axis=1.2, cex=1.3, lwd=1)
Error in start(unlist(genomicData)) : 
  error in evaluating the argument 'x' in selecting a method for function 'start': Error in unlist(genomicData) : argument not a list

Could this error have something to do with the warning that Im getting: 

dxd <- estimateDispersions( dxd )
using supplied model matrix
using supplied model matrix
Warning message:
In estimateDispersionsFit(object, fitType = fitType, quiet = quiet) :
  the parametric fit of dispersion estimates over the mean of counts
failed, which occurs when the trend is not well captured by the
function y = a/x + b. A local regression fit is automatically performed,
and the analysis can continue. You can specify fitType='local' or 'mean'
to avoid this message if re-running the same data.
When using local regression fit, the user should examine plotDispEsts(dds)
to make sure the fitted line is not sharply curving up or down based on
the position of individual points.

I tried plotting the dispersion (using plotDispEsts) and it doesn't look too alarming so the error sounds unrelated to me. (let me know if it would be helpful to upload it) 

Any help would be very much appreciated! Many thanks in advance for your reply!

Best wishes,

Emmanouela

Here is my code: 

dxd <- DEXSeqDataSetFromHTSeq(my_samples, sampleData=sample_ids, flattenedfile=my_gft, design= ~ sample + exon + Tissue:exon ) # I am looking at DEU in different tissues (and my sample_ids have a column named Tissue instead of condition)
dxd <- estimateSizeFactors( dxd )
dxd <- estimateDispersions( dxd )
plotDispEsts( dxd )

dxd <- testForDEU( dxd )
dxd <- estimateExonFoldChanges( dxd, fitExpToVar="Tissue")
dxr1 <- DEXSeqResults( dxd )
plotDEXSeq(dxr1, "ENSG00000163660", displayTranscripts=T,legend=TRUE,  cex.axis=1.2, cex=1.3, lwd=1)

And here is my sessionInfo():

sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.ISO-8859-1       LC_NUMERIC=C                    LC_TIME=en_GB.ISO-8859-1        LC_COLLATE=en_GB.ISO-8859-1    
 [5] LC_MONETARY=en_GB.ISO-8859-1    LC_MESSAGES=en_GB.ISO-8859-1    LC_PAPER=C                      LC_NAME=C                      
 [9] LC_ADDRESS=C                    LC_TELEPHONE=C                  LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C            

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.10.6             BiocParallel_0.4.1        DESeq2_1.4.5              RcppArmadillo_0.4.450.1.0 Rcpp_0.11.3              
 [6] GenomicRanges_1.14.4      XVector_0.2.0             IRanges_1.20.7            Biobase_2.22.0            BiocGenerics_0.8.0       

loaded via a namespace (and not attached):
 [1] annotate_1.40.1      AnnotationDbi_1.24.0 BatchJobs_1.4        BBmisc_1.7           biomaRt_2.18.0       Biostrings_2.30.1   
 [7] bitops_1.0-6         brew_1.0-6           checkmate_1.4        codetools_0.2-9      DBI_0.3.1            digest_0.6.4        
[13] fail_1.2             foreach_1.4.2        genefilter_1.44.0    geneplotter_1.40.0   grid_3.0.1           hwriter_1.3.2       
[19] iterators_1.0.7      lattice_0.20-29      locfit_1.5-9.1       RColorBrewer_1.0-5   RCurl_1.95-4.3       Rsamtools_1.14.3    
[25] RSQLite_0.11.4       sendmailR_1.2-1      splines_3.0.1        statmod_1.4.20       stats4_3.0.1         stringr_0.6.2       
[31] survival_2.37-7      tools_3.0.1          XML_3.98-1.1         xtable_1.7-4         zlibbioc_1.8.0      

Hi Emmanouela,

Could you include the code you used to generate your DEXSeqDataSet object?

Alejandro