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Old 02-05-2016, 11:40 AM   #1
icanwinwyz
Junior Member
 
Location: LA

Join Date: Feb 2016
Posts: 8
Default HELP!!DEXseq error from DEXSeqResults

Hi,
I am using DEXSeq to do alternative splicing analysis. But when I use the test data from DEXSeq's package, I even got an error from the function "DEXSeqResults". I have no idea why this error occurs. Could anyone help me?

The code I used is shown below:

> library(DEXSeq)
> data(pasillaDEXSeqDataSet, package="pasilla")
> dxd <- estimateSizeFactors( dxd )
> dxd <- estimateDispersions( dxd )
using supplied model matrix
using supplied model matrix
> dxd <- testForDEU( dxd )
using supplied model matrix
> dxr <- DEXSeqResults( dxd )
Error in (function (cl, name, valueClass) :
assignment of an object of class “NULL” is not valid for @‘elementMetadata’ in an object of class “GRanges”; is(value, "DataFrame") is not TRUE
>
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Old 02-05-2016, 12:32 PM   #2
blancha
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Location: Montreal

Join Date: May 2013
Posts: 367
Default

The first step when a bug is encountered is always to update to the latest version of the program available, before reporting the bug.

Check your version of DEXSeq.
If it's not 1.16.8, start by updating DEXSeq first.
Unfortunately, that may involve updating R and Bioconductor.

Code:
packageVersion("DEXSeq")
The second step when reporting a bug in R, is posting your session info, with the bug.

Code:
sessionInfo()
Incidentally, your code works fine for me with DEXSeq 1.16.8.
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Old 02-05-2016, 12:50 PM   #3
icanwinwyz
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Location: LA

Join Date: Feb 2016
Posts: 8
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Quote:
Originally Posted by blancha View Post
The first step when a bug is encountered is always to update to the latest version of the program available, before reporting the bug.

Check your version of DEXSeq.
If it's not 1.16.8, start by updating DEXSeq first.
Unfortunately, that may involve updating R and Bioconductor.

Code:
packageVersion("DEXSeq")
The second step when reporting a bug in R, is posting your session info, with the bug.

Code:
sessionInfo()
Incidentally, your code works fine for me with DEXSeq 1.16.8.
Hi blancha,
Thanks for your reply. Yes, I indeed checked the version of DEXseq and R. Everything is up-to-date shown below:

> version
......
major 3
minor 2.3
year 2015
month 12
day 10
svn rev 69752
language R
version.string R version 3.2.3 (2015-12-10)


> packageVersion("DEXSeq")
[1] ‘1.16.8’

I searched online and didn't find the solution to this problem. You have some other ideas? Thanks!
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Old 02-05-2016, 01:05 PM   #4
dpryan
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Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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You presumably have an outdated dependency. What you tried works for me without an error. My setup is below:
Code:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

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] DEXSeq_1.16.8              DESeq2_1.10.1             
 [3] RcppArmadillo_0.6.500.4.0  Rcpp_0.12.3               
 [5] SummarizedExperiment_1.0.2 GenomicRanges_1.22.4      
 [7] GenomeInfoDb_1.6.3         IRanges_2.4.6             
 [9] S4Vectors_0.8.11           Biobase_2.30.0            
[11] BiocGenerics_0.16.1        BiocParallel_1.4.3        
[13] BiocInstaller_1.20.1      


loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.3          
 [4] XVector_0.10.0       bitops_1.0-6         futile.options_1.0.0
 [7] tools_3.2.3          zlibbioc_1.16.0      biomaRt_2.26.1      
[10] statmod_1.4.24       rpart_4.1-10         RSQLite_1.0.0       
[13] annotate_1.48.0      gtable_0.1.2         lattice_0.20-33     
[16] DBI_0.3.1            gridExtra_2.0.0      stringr_1.0.0       
[19] hwriter_1.3.2        genefilter_1.52.1    cluster_2.0.3       
[22] Biostrings_2.38.3    locfit_1.5-9.1       grid_3.2.3          
[25] nnet_7.3-12          AnnotationDbi_1.32.3 XML_3.98-1.3        
[28] survival_2.38-3      foreign_0.8-66       latticeExtra_0.6-26 
[31] Formula_1.2-1        magrittr_1.5         geneplotter_1.48.0  
[34] ggplot2_2.0.0        lambda.r_1.1.7       Rsamtools_1.22.0    
[37] Hmisc_3.17-1         scales_0.3.0         splines_3.2.3       
[40] xtable_1.8-2         colorspace_1.2-6     stringi_1.0-1       
[43] acepack_1.3-3.3      RCurl_1.95-4.7       munsell_0.4.2
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Old 02-05-2016, 01:31 PM   #5
blancha
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Location: Montreal

Join Date: May 2013
Posts: 367
Default

I agree with dpryan.
sessionInfo() will give more details about the attached packages.
Check which packages differ from our setup.
Perhaps you just need to update GenomicRanges.
In the worse case scenario, you can just update everything or reinstall everything.
The code works fine for me.

Code:
> library(DEXSeq)
> data(pasillaDEXSeqDataSet, package="pasilla")
> dxd <- estimateSizeFactors( dxd )
> dxd <- estimateDispersions( dxd )
using supplied model matrix
using supplied model matrix
> dxd <- testForDEU( dxd )
using supplied model matrix
> dxr <- DEXSeqResults( dxd )
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

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

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

other attached packages:
 [1] DEXSeq_1.16.7              DESeq2_1.10.1             
 [3] RcppArmadillo_0.6.400.2.2  Rcpp_0.12.3               
 [5] SummarizedExperiment_1.0.2 GenomicRanges_1.22.3      
 [7] GenomeInfoDb_1.6.1         IRanges_2.4.6             
 [9] S4Vectors_0.8.7            Biobase_2.30.0            
[11] BiocGenerics_0.16.1        BiocParallel_1.4.3        
[13] nvimcom_0.9-8             

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.3          
 [4] XVector_0.10.0       bitops_1.0-6         futile.options_1.0.0
 [7] tools_3.2.1          zlibbioc_1.16.0      biomaRt_2.26.1      
[10] statmod_1.4.23       rpart_4.1-10         RSQLite_1.0.0       
[13] annotate_1.48.0      gtable_0.1.2         lattice_0.20-33     
[16] DBI_0.3.1            gridExtra_2.0.0      stringr_1.0.0       
[19] hwriter_1.3.2        genefilter_1.52.0    cluster_2.0.3       
[22] Biostrings_2.38.3    locfit_1.5-9.1       grid_3.2.1          
[25] nnet_7.3-11          AnnotationDbi_1.32.3 XML_3.98-1.3        
[28] survival_2.38-3      foreign_0.8-66       latticeExtra_0.6-26 
[31] Formula_1.2-1        magrittr_1.5         geneplotter_1.48.0  
[34] ggplot2_2.0.0        lambda.r_1.1.7       Rsamtools_1.22.0    
[37] Hmisc_3.17-1         scales_0.3.0         splines_3.2.1       
[40] xtable_1.8-0         colorspace_1.2-6     stringi_1.0-1       
[43] acepack_1.3-3.3      RCurl_1.95-4.7       munsell_0.4.2
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