Hello all,

I am working on a simple DEU case for Arabidopsis and have run into an error with DEXSeqHTML.  Everything runs fine until I try and call DEXSeqHTML on my DEXSeqResults object and I get an error of 

Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

I looked through the code displayed when calling DEXSeqResults to no avail, and am feeling a bit stuck :/.  Things that may be important; I am using DEXSeq 1.14.1 and R 3.2.0.  No errors occur during the execution of the prior code, although my dispersion failed to fit the normal regression .   My gff was built from the TAIR10_16 release using the HTSeq pipeline provided in the vignette.  Although I did run the dexseq_count.py on each technical replicate, and then summed each tech rep and wrote them to file in a format similar to that of the normal output (no errors so I assume I did this correctly).  As a liner note I will eventually use the individual tech reps but want to get a feel for DEXSeq before implementing the more complex models.  I have not downloaded and run the sample data.

Thank you for your time.

Sam

Session Info:

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.14.1             DESeq2_1.8.1              RcppArmadillo_0.5.200.1.0 Rcpp_0.11.6               GenomicRanges_1.20.5     
 [6] GenomeInfoDb_1.4.1        IRanges_2.2.5             S4Vectors_0.6.1           Biobase_2.28.0            BiocGenerics_0.14.0      
[11] BiocParallel_1.2.9       

loaded via a namespace (and not attached):
 [1] genefilter_1.50.0    statmod_1.4.21       locfit_1.5-9.1       reshape2_1.4.1       splines_3.2.0        lattice_0.20-31     
 [7] colorspace_1.2-6     survival_2.38-3      XML_3.98-1.3         foreign_0.8-65       DBI_0.3.1            RColorBrewer_1.1-2  
[13] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0        zlibbioc_1.14.0      Biostrings_2.36.1    munsell_0.4.2       
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2        latticeExtra_0.6-26  geneplotter_1.46.0   biomaRt_2.24.0      
[25] AnnotationDbi_1.30.1 proto_0.3-10         acepack_1.3-3.3      xtable_1.7-4         scales_0.2.5         Hmisc_3.16-0        
[31] annotate_1.46.0      XVector_0.8.0        Rsamtools_1.20.4     gridExtra_0.9.1      ggplot2_1.0.1        digest_0.6.8        
[37] stringi_0.5-5        grid_3.2.0           tools_3.2.0          bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7      
[43] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.2        futile.options_1.0.0 MASS_7.3-42          rpart_4.1-10        
[49] nnet_7.3-10 

Relevant Code:

Leaf = countFls[7:12]
DescLeaf = sampleDesc[7:12,] #  CS, CST
TissueWiseModel    = ~sample + exon + Treatment:exon
Ldxd = DEXSeqDataSetFromHTSeq(
  countfiles = Leaf,        # vector of count file names
  sampleData = DescLeaf,    # description of said files
  design = TissueWiseModel, # formula for testing
  flattenedfile = gffPath)  # gff used for creating aln files
Ldxd = estimateSizeFactors(Ldxd)
Ldxd = estimateDispersions(Ldxd, BPPARAM=BPPARAM)
Ldxd = testForDEU(Ldxd, BPPARAM=BPPARAM)
Ldxd = estimateExonFoldChanges(Ldxd, fitExpToVar = "Treatment", BPPARAM=BPPARAM)
Ldxr1 = DEXSeqResults(Ldxd)
DEXSeqHTML( object =Ldxr1, FDR=0.05, color=c("#FF000080", "#0000FF80"),BPPARAM=BPPARAM)