DEXSeqHTML output issue

[phred]

After running the DEXSeqHTML command on my exonCountDataset, I get the folder called DEXSeqReport containing the files as expected.

However, when I open the testForDEU.html file, the links to the individual exon files from the testForDEU result table (counts, expression etc) don't work.

Firefox can't find the file at 
/Sequencing/results and plots/dexseq/
DEXSeqReport/files/ENSG00000005381expression.svg.

Has anyone any suggestions? If so, I'd be grateful.

> sessionInfo()
R version 3.0.0 RC (2013-03-26 r62418)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] RCurl_1.95-4.1     bitops_1.0-5       pasilla_0.2.16     DESeq_1.11.6
[5] lattice_0.20-15    locfit_1.5-9       DEXSeq_1.6.0       Biobase_2.19.3
[9] BiocGenerics_0.5.6

loaded via a namespace (and not attached):
 [1] annotate_1.37.4       AnnotationDbi_1.21.16 biomaRt_2.16.0
 [4] Biostrings_2.28.0     Cairo_1.5-2           DBI_0.2-5
 [7] genefilter_1.41.3     geneplotter_1.37.0    GenomicRanges_1.11.41
[10] grid_3.0.0            hwriter_1.3           IRanges_1.17.41
[13] RColorBrewer_1.0-5    Rsamtools_1.12.0      RSQLite_0.11.2
[16] splines_3.0.0         statmod_1.4.17        stats4_3.0.0
[19] stringr_0.6.2         survival_2.37-4       tools_3.0.0
[22] XML_3.96-0.2          xtable_1.7-1          zlibbioc_1.6.0

[Simon Anders]

So, does the file exist at the position indicated by the error message?

[phred]

So, does the file exist at the position indicated by the error message?

I appreciate your reply.

Yes the files are created but the only .html file containing information for a particular gene is geneIDresults.html. Counts, expression, splicing and transcripts don't contain information.

Is it that I need to have run the various plotDEXSeq commands (splicing, counts, expression, transcripts) for each individual gene beforehand and the DEXSeqHTML command pulls from these. I have 108 significant genes at an FDR 0.1.

The link to the example contained in the vignette:

http://www.embl.de/~reyes/DEXSeqReport/testForDEU.html.

is broken, so I was a little unsure as to what the end result should be.

[areyes]

Hi phred,

1. Could you include an example with your code?
2. Are you able to run and succesfully display the example from the function?

data("pasillaExons", package="pasilla")
pasillaExons <- estimateSizeFactors( pasillaExons )
pasillaExons <- estimateDispersions( pasillaExons )
pasillaExons <- fitDispersionFunction( pasillaExons )
pasillaExons <- testForDEU( pasillaExons )
DEXSeqHTML( pasillaExons )

[phred]

Thank you for your reply.

When I run the pasilla example as you suggested, I get the following:

> data("pasillaExons", package="pasilla")
> pasillaExons <- estimateSizeFactors( pasillaExons )
> pasillaExons <- estimateDispersions( pasillaExons, nCores = 8 )
Estimating Cox-Reid exon dispersion estimates using 8 cores. (Progress report: one dot per 100 genes)
> pasillaExons <- fitDispersionFunction( pasillaExons )
> pasillaExons <- testForDEU( pasillaExons )
Testing for differential exon usage. (Progress report: one dot per 100 genes)

> DEXSeqHTML( pasillaExons )
There were 25 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In svg(paste(ptowrite, pagename, onlytag, ".svg", sep = ""),  ... :
  unable to load shared object '/home/support/apps/cports/rhel-6.x86_64/gnu/R/3.0.0.RC/lib64/R/library/grDevices/libs//cairo.so':
  /home/support/apps/cports/rhel-6.x86_64/gnu/R/3.0.0.RC/lib64/R/library/grDevices/libs//cairo.so: cannot open shared object file: No such file or directory
2: In svg(paste(ptowrite, pagename, onlytag, ".svg", sep = ""),  ... :
  failed to load cairo DLL
3: In svg(paste(ptowrite, pagename, onlytag, ".svg", sep = ""),  ... :
  failed to load cairo DLL
4: In svg(paste(ptowrite, pagename, onlytag, ".svg", sep = ""),  ... :
  failed to load cairo DLL
[etc ....]

> sessionInfo()
R version 3.0.0 RC (2013-03-26 r62418)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] DESeq_1.11.6       lattice_0.20-15    locfit_1.5-9       DEXSeq_1.6.0
[5] Biobase_2.19.3     BiocGenerics_0.5.6

loaded via a namespace (and not attached):
 [1] annotate_1.37.4       AnnotationDbi_1.21.16 biomaRt_2.16.0
 [4] Biostrings_2.28.0     bitops_1.0-5          DBI_0.2-5
 [7] genefilter_1.41.3     geneplotter_1.37.0    GenomicRanges_1.11.41
[10] grid_3.0.0            hwriter_1.3           IRanges_1.17.41
[13] RColorBrewer_1.0-5    RCurl_1.95-4.1        Rsamtools_1.12.0
[16] RSQLite_0.11.2        splines_3.0.0         statmod_1.4.17
[19] stats4_3.0.0          stringr_0.6.2         survival_2.37-4
[22] XML_3.96-0.2          xtable_1.7-1          zlibbioc_1.6.0

Similarly, now when I run my own example, I am getting:

> DEXSeqHTML(ecs)
Error in .External.graphics(C_layout, num.rows, num.cols, mat, as.integer(num.figures),  :
  invalid graphics state
In addition: There were 50 or more warnings (use warnings() to see the first 50)

> warnings()
Warning messages:
1: In svg(paste(ptowrite, pagename, onlytag, ".svg", sep = ""),  ... :
  unable to load shared object '/home/support/apps/cports/rhel-6.x86_64/gnu/R/3.0.0.RC/lib64/R/library/grDevices/libs//cairo.so':
  /home/support/apps/cports/rhel-6.x86_64/gnu/R/3.0.0.RC/lib64/R/library/grDevices/libs//cairo.so: cannot open shared object file: No such file or directory
2: In svg(paste(ptowrite, pagename, onlytag, ".svg", sep = ""),  ... :
  failed to load cairo DLL
[etc...]

I installed the package Cairo and re-ran the command but it didn't make a difference.

[Simon Anders]

Your problem has nothing to do with DEXSeq, it seems, rather with your R installation.

Try this minimal example, which on a proper installation, will produce an SVG file with a plot of a bell curve:

svg( "bell.svg" )
plot( dnorm, xlim=c(-5,5) )
dev.off()

It seems that you have a non-standard R installation ("/home/support/apps/cports/rhel-6.x86_64/gnu/..."), and it most likely was not correctly compiled/linked against Cairo. If you did the install yourself, try again, following the R installation instructions carefully (and better use a pre-compiled one this time); if it was done by your IT group, you'll have to get them to fix it.

[phred]

Thanks for your advice.

I will ask our IT people to look into this.