DEXSeq error while creating ExonCountSet object

Question

[mtiwari]

Hi

I am using DEXSeq for my analysis.

However, I am facing error while making the ExonCountSet object for further processing.

Specifically, on running

ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, dros_flattened.gff)

I get the error:

Error in checkAtAssignment("character", "annotationFile", "character") :
  'annotationFile' is not a slot in class "character"
In addition: Warning message:
'newExonCountSet' is deprecated.
Use 'DEXSeqDataSet' instead.
See help("Deprecated")

I prepared the gff file using the dexseq python script, and all other steps alsp as in the DEXSeq vignette.

Any suggestions/workarounds are most welcome.

Thanks
M

[Devon Ryan]

What's the output of sessionInfo()? It's likely that you just need to update all of the packages.

[mtiwari]

The output of sessionInfo()

>sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
 [1] DEXSeq_1.10.3           BiocParallel_0.6.0      DESeq2_1.4.5
 [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1             GenomicRanges_1.16.3
 [7] GenomeInfoDb_1.0.2      IRanges_1.22.6          Biobase_2.24.0
[10] BiocGenerics_0.10.0     BiocInstaller_1.14.2

loaded via a namespace (and not attached):
 [1] annotate_1.42.0      AnnotationDbi_1.26.0 BatchJobs_1.2
 [4] BBmisc_1.6           biomaRt_2.20.0       Biostrings_2.32.0
 [7] bitops_1.0-6         brew_1.0-6           codetools_0.2-8
[10] DBI_0.2-7            digest_0.6.4         fail_1.2
[13] foreach_1.4.2        genefilter_1.46.1    geneplotter_1.42.0
[16] grid_3.1.0           hwriter_1.3          iterators_1.0.7
[19] lattice_0.20-29      locfit_1.5-9.1       plyr_1.8.1
[22] RColorBrewer_1.0-5   RCurl_1.95-4.1       Rsamtools_1.16.0
[25] RSQLite_0.11.4       sendmailR_1.1-2      splines_3.1.0
[28] statmod_1.4.19       stats4_3.1.0         stringr_0.6.2
[31] survival_2.37-7      tools_3.1.0          XML_3.98-1.1
[34] xtable_1.7-3         XVector_0.4.0        zlibbioc_1.10.0

[mtiwari]

If I try to check the package status using,

> inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]

I get:

	Package Version Status
	annotate annotate 1.42.0 unavailable
	AnnotationDbi AnnotationDbi 1.26.0 unavailable
	Biobase Biobase 2.24.0 unavailable
	BiocGenerics BiocGenerics 0.10.0 unavailable
	BiocInstaller BiocInstaller 1.14.2 unavailable
	BiocParallel BiocParallel 0.6.0 unavailable
	biomaRt biomaRt 2.20.0 unavailable
	Biostrings Biostrings 2.32.0 unavailable
	biovizBase biovizBase 1.12.1 unavailable
	BSgenome BSgenome 1.32.0 unavailable
	cummeRbund cummeRbund 2.6.0 unavailable
	DESeq DESeq 1.16.0 unavailable
	DESeq2 DESeq2 1.4.5 unavailable
	DEXSeq DEXSeq 1.10.3 unavailable
	drosgenome1.db drosgenome1.db 2.14.0 unavailable
	EBSeq EBSeq 1.4.0 unavailable
	edgeR edgeR 3.6.2 unavailable
	gage gage 2.14.0 unavailable
	gageData gageData 2.2.0 unavailable
	genefilter genefilter 1.46.1 unavailable
	geneplotter geneplotter 1.42.0 unavailable
	GenomeInfoDb GenomeInfoDb 1.0.2 unavailable
	GenomicAlignments GenomicAlignments 1.0.1 unavailable
	GenomicFeatures GenomicFeatures 1.16.0 unavailable
	GenomicRanges GenomicRanges 1.16.3 unavailable
	GO.db GO.db 2.14.0 unavailable
	graph graph 1.42.0 unavailable
	Gviz Gviz 1.8.2 unavailable
	hgu133a.db hgu133a.db 2.14.0 unavailable
	hgu133plus2.db hgu133plus2.db 2.14.0 unavailable
	hgu95av2.db hgu95av2.db 2.14.0 unavailable
	impute impute 1.38.1 unavailable
	IRanges IRanges 1.22.6 unavailable
	KEGG.db KEGG.db 2.14.0 unavailable
	KEGGREST KEGGREST 1.4.0 unavailable
	limma limma 3.20.3 unavailable
	manipulate manipulate 0.98.507 unavailable
	minet minet 3.20.0 unavailable
	OrderedList OrderedList 1.36.0 unavailable
	org.Bt.eg.db org.Bt.eg.db 2.14.0 unavailable
	org.Ce.eg.db org.Ce.eg.db 2.14.0 unavailable
	org.Cf.eg.db org.Cf.eg.db 2.14.0 unavailable
	org.Dm.eg.db org.Dm.eg.db 2.14.0 unavailable
	org.Dr.eg.db org.Dr.eg.db 2.14.0 unavailable
	org.Gg.eg.db org.Gg.eg.db 2.14.0 unavailable
	org.Hs.eg.db org.Hs.eg.db 2.14.0 unavailable
	org.Mm.eg.db org.Mm.eg.db 2.14.0 unavailable
	org.Rn.eg.db org.Rn.eg.db 2.14.0 unavailable
	org.Sc.sgd.db org.Sc.sgd.db 2.14.0 unavailable
	Rsamtools Rsamtools 1.16.0 unavailable
	rstudio rstudio 0.98.507 unavailable
	rtracklayer rtracklayer 1.24.1 unavailable
	SNPlocs.Hsapiens.dbSNP.20100427 SNPlocs.Hsapiens.dbSNP.20100427 0.99.6 unavailable
	topGO topGO 2.16.0 unavailable
	twilight twilight 1.40.0 unavailable
	VariantAnnotation VariantAnnotation 1.10.1 unavailable
	XVector XVector 0.4.0 unavailable
	zlibbioc zlibbioc 1.10.0 unavailable

view raw biostars-101224.txt hosted with ❤ by GitHub

Does it indicate that all the packages are uptodate, or otherwise?

Thanks
M

[mtiwari]

Thank You Devon.

The ecs data object is successfully created.

But shouldn't deprecated packages be automatically removed, or the authors have not updated the vignette (I am following the DEXSeq vignettte (last revision: 2013-10-08)).

And that's probably why I am now running into following errors:

> head( fData(ecs)$dispBeforeSharing )
Error in head(fData(ecs)$dispBeforeSharing) :
  error in evaluating the argument 'x' in selecting a method for function 'head': Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'fData' for signature '"character"'
> ecs@dispFitCoefs
Error: trying to get slot "dispFitCoefs" from an object of a basic class ("character") with no slots
> head( fData(ecs)$dispFitted )
Error in head(fData(ecs)$dispFitted) :
  error in evaluating the argument 'x' in selecting a method for function 'head': Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'fData' for signature '"character"'
> plotDispEsts( ecs )
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'plotDispEsts' for signature '"character"'
> ecs <- testForDEU( ecs )
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'sizeFactors' for signature '"character"'

Do you know of any current versions of the vignette, or a way around to solve these errors?

Thanks again
M

[Devon Ryan]

Hi M,

It looks like Alejandro forgot to remove the read.HTSeqCount() function from the source, even though it's set as being deprecated itself. Anyway, the vignette you're looking at is older than the version you have. If you just type vignette("DEXSeq") from within R you'll get the current one (it's already on your hard drive). You'll note that it lacks the read.HTSeqCounts() function. Further, the ExonCountSet (what the ecs variable stands for) class has itself been deprecated, so you're trying to use its accessors on a DEXSeqDataSet object (which is just an extension of a DESeqDataSet object). Have a look through the updated vignette and your life will be much easier :)

[mtiwari]

Thanks Devon for pointing in the right direction.

Answer 1

[Devon Ryan]

This is likely due to you using a deprecated function for the version of DEXseq you have. read.HTSeqCounts() was replaced by DEXSeqDataSetFromHTSeq(), so try that instead.