Question: DEXSeq Error when calculating Exon Fold-changes
0
gravatar for Assa Yeroslaviz
3.8 years ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:

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
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Assa Yeroslaviz1.4k

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)

ADD REPLYlink written 3.8 years ago by Assa Yeroslaviz1.4k
1

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

ADD REPLYlink written 3.8 years ago by Alejandro Reyes1.7k

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  
ADD REPLYlink written 3.8 years ago by Assa Yeroslaviz1.4k
Answer: DEXSeq Error when calculating Exon Fold-changes
0
gravatar for Assa Yeroslaviz
3.8 years ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:

Thanks Alejandro.

that solve the problem!

ADD COMMENTlink written 3.8 years ago by Assa Yeroslaviz1.4k
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