DEXSeq Error when calculating Exon Fold-changes
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 19 days ago
Munich, Germany

Hi,

 

I am running DEXSeq (DEXSeq_1.12.2) and getting an error message, when trying to calculate the Exon fold-changes.

I have tried both the single commands-method as well as the DEXSeq() wrapper. the script I am using as well as the sessionInfo are added at the bottom.

In both cases ( for the wrapper I can only assume) I am getting the following error message when calculating the exon fold-changes

using supplied model matrix
...
using supplied model matrix
using supplied model matrix
Error in exp(alleffects) : non-numeric argument to mathematical function

As the complete dataset is too big to run multiple times, I have created a subset with only the first 1000 genes, but it still gives me the error message.

Does it has anything to do with the sampleTable I am using?

> CR4W0h.CTRL0hsampleTable
   sampleName treatment replica timepoint condition
11     CR4Wo1     CR4Wo       1        0h   CR4Wo0h
12     CR4Wo2     CR4Wo       2        0h   CR4Wo0h
13     CR4Wo3     CR4Wo       3        0h   CR4Wo0h
14     CR4Wo4     CR4Wo       4        0h   CR4Wo0h
1         C20      ctrl       1        0h    ctrl0h
2         C22      ctrl       2        0h    ctrl0h
3         C23      ctrl       3        0h    ctrl0h
4         C24      ctrl       4        0h    ctrl0h

 

Thanks a lot for any help,

Assa

 

Here is my script:

# creating the DEXSeq object
CR4W0h.CTRL0hdxd <- DEXSeqDataSetFromHTSeq(CR4W0h.CTRL0hfiles,
+                                            sampleData = CR4W0h.CTRL0hsampleTable,
+                                            design = ~sample + exon + treatment:exon,
+                                            flattenedfile = flattenedFile)

# use the single command mode:
CR4W0h.CTRL0hdxd = estimateSizeFactors( dxdtest )
CR4W0h.CTRL0hdxd = estimateDispersions( CR4W0h.CTRL0hdxd, BPPARAM=BPPARAM)
CR4W0h.CTRL0hdxd = testForDEU( CR4W0h.CTRL0hdxd, BPPARAM=BPPARAM )
CR4W0h.CTRL0hdxd = estimateExonFoldChanges( CR4W0h.CTRL0hdxd, fitExpToVar="treatment", BPPARAM=BPPARAM)
CR4W0h.CTRL0hdxr <- DEXSeqResults(object = CR4W0h.CTRL0hdxd)
# using the wrapper command
CR4W0h.CTRL0hdxd <- DEXSeq(object = CR4W0h.CTRL0hdxd, fullModel = ~sample + exon + treatment:exon,BPPARAM = BPPARAM, fitExpToVar = "treatment" )

> 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
 [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=en_US.UTF-8       LC_NAME=C
 [9] 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
[8] methods   base

other attached packages:
 [1] rtracklayer_1.26.3        DEXSeq_1.12.2
 [3] BiocParallel_1.0.3        DESeq2_1.6.3
 [5] RcppArmadillo_0.6.200.2.0 Rcpp_0.12.2
 [7] GenomicRanges_1.18.4      GenomeInfoDb_1.2.5
 [9] IRanges_2.0.1             S4Vectors_0.4.0
[11] Biobase_2.26.0            BiocGenerics_0.12.1
[13] BiocInstaller_1.16.5

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         annotate_1.44.0         AnnotationDbi_1.28.2
 [4] base64enc_0.1-3         BatchJobs_1.6           BBmisc_1.9
 [7] biomaRt_2.22.0          Biostrings_2.34.1       bitops_1.0-6
[10] brew_1.0-6              checkmate_1.6.3         cluster_2.0.3
[13] codetools_0.2-14        colorspace_1.2-6        DBI_0.3.1
[16] digest_0.6.8            fail_1.3                foreach_1.4.3
[19] foreign_0.8-66          Formula_1.2-1           genefilter_1.48.1
[22] geneplotter_1.44.0      GenomicAlignments_1.2.2 ggplot2_1.0.1
[25] grid_3.1.0              gridExtra_2.0.0         gtable_0.1.2
[28] Hmisc_3.17-0            hwriter_1.3.2           iterators_1.0.8
[31] lattice_0.20-33         latticeExtra_0.6-26     locfit_1.5-9.1
[34] magrittr_1.5            MASS_7.3-45             munsell_0.4.2
[37] nnet_7.3-11             plyr_1.8.3              proto_0.3-10
[40] RColorBrewer_1.1-2      RCurl_1.95-4.7          reshape2_1.4.1
[43] rpart_4.1-10            Rsamtools_1.18.3        RSQLite_1.0.0
[46] scales_0.3.0            sendmailR_1.2-1         splines_3.1.0
[49] statmod_1.4.22          stringi_1.0-1           stringr_1.0.0
[52] survival_2.38-3         tools_3.1.0             XML_3.98-1.3
[55] xtable_1.8-0            XVector_0.6.0           zlibbioc_1.12.0
dexseq logfoldchange exon usage • 926 views
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interestingly it happens on the Ubuntu (14.04.3) server, but not on my iMac (which break down if I try to run the whole data set)

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Hi Assa,

1. Could you try to update your R and Bioconductor to either the release version or the development version, and see if the error persists?

2. Can you include the sessionInfo() from your iMac?

Alejandro

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I added the seesionInfo() from my iMac below

 

I am now updating the R vesrion on my server

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] DEXSeq_1.16.1              DESeq2_1.10.0              RcppArmadillo_0.6.200.2.0  Rcpp_0.12.2                SummarizedExperiment_1.0.1
 [6] GenomicRanges_1.22.1       GenomeInfoDb_1.6.1         IRanges_2.4.1              S4Vectors_0.8.2            Biobase_2.30.0            
[11] BiocGenerics_0.16.1        BiocParallel_1.4.0        

loaded via a namespace (and not attached):
 [1] genefilter_1.52.0    statmod_1.4.22       locfit_1.5-9.1       reshape2_1.4.1       splines_3.2.2        lattice_0.20-33      colorspace_1.2-6    
 [8] survival_2.38-3      XML_3.98-1.3         foreign_0.8-66       DBI_0.3.1            RColorBrewer_1.1-2   lambda.r_1.1.7       plyr_1.8.3          
[15] stringr_1.0.0        zlibbioc_1.16.0      Biostrings_2.38.0    munsell_0.4.2        gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2       
[22] latticeExtra_0.6-26  geneplotter_1.48.0   biomaRt_2.26.0       AnnotationDbi_1.32.0 proto_0.3-10         acepack_1.3-3.3      xtable_1.8-0        
[29] scales_0.3.0         Hmisc_3.17-0         annotate_1.48.0      XVector_0.10.0       Rsamtools_1.22.0     gridExtra_2.0.0      ggplot2_1.0.1       
[36] digest_0.6.8         stringi_1.0-1        grid_3.2.2           tools_3.2.2          bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7      
[43] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3        futile.options_1.0.0 MASS_7.3-45          rpart_4.1-10         nnet_7.3-11  
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 19 days ago
Munich, Germany

Thanks Alejandro.

that solve the problem!

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