Search
Question: Error: non-character argument in DEXSeqDataSetFromHTSeq from DEXSeq
0
gravatar for arom2
2.4 years ago by
arom20
United States
arom20 wrote:

To Whom It May Concern, 
I am currently working out the pipeline for differential expression on a subset of RNA-seq lists (2 treatments with 2 biological replicates each) and following the pasilla tutorial online. I am encountering an error with the DEXSeq Bioconductor package when creating the object "DEXSeqDataSetFromHTSeq". I have changed a few names (files and paths) for confidentiality and clarity purposes!

Error:
Error in strsplit(rownames(dcounts), ":") : non-character argument

>inDir = "/home/user"

>countFiles = list.files(inDir, pattern="sorted.txt", full.names=TRUE)
>countFiles
[1] "/home/user/x1_pe_align_sorted.txt"
[2] "/home/user/x2_pe_align_sorted.txt" 
[3] "/home/user/y1_pe_align_sorted.txt" 
[4] "/home/user/y2_pe_align_sorted.txt"

>flattenedFile = list.files(inDir, pattern="gff$", full.names=TRUE)
>flattenedFile
[1] "/home/user/GCF_Reference_from_NCBI.gff"

> sampleTable = data.frame(row.names = c( "x1", "x2", "y1","y2"),condition = c("x_tx", "x_tx", "y_tx","y_tx" ), libType = c( "paired-end", "paired-end","paired-end", "paired-end" ) )
> sampleTable
                               condition    libType
/home/user/x1_pe_align_sorted.txt   x_tx paired-end
/home/user/x2_pe_align_sorted.txt   x_tx paired-end
/home/user/y1_pe_align_sorted.tx    y_tx paired-end
/home/user/y2_pe_align_sorted.txt   y_tx paired-end

>dxd = DEXSeqDataSetFromHTSeq(countfiles=countFiles,sampleData=sampleTable,design=~ sample + exon + condition:exon,flattenedfile=flattenedFile )
Error in strsplit(rownames(dcounts), ":") : non-character argument


> 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_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_1.14.1             DESeq2_1.8.1             
 [3] RcppArmadillo_0.5.200.1.0 Rcpp_0.12.0              
 [5] GenomicRanges_1.20.5      GenomeInfoDb_1.4.1       
 [7] IRanges_2.2.5             S4Vectors_0.6.3          
 [9] Biobase_2.28.0            BiocGenerics_0.14.0      
[11] BiocParallel_1.2.9        BiocInstaller_1.18.4     

loaded via a namespace (and not attached):
 [1] genefilter_1.50.0    statmod_1.4.21       locfit_1.5-9.1      
 [4] reshape2_1.4.1       splines_3.2.1        lattice_0.20-33     
 [7] colorspace_1.2-6     survival_2.38-3      XML_3.98-1.3        
[10] foreign_0.8-65       DBI_0.3.1            RColorBrewer_1.1-2  
[13] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0       
[16] zlibbioc_1.14.0      Biostrings_2.36.1    munsell_0.4.2       
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2       
[22] latticeExtra_0.6-26  geneplotter_1.46.0   biomaRt_2.24.0      
[25] AnnotationDbi_1.30.1 proto_0.3-10         acepack_1.3-3.3     
[28] xtable_1.7-4         scales_0.2.5         Hmisc_3.16-0        
[31] annotate_1.46.1      XVector_0.8.0        Rsamtools_1.20.4    
[34] gridExtra_2.0.0      ggplot2_1.0.1        digest_0.6.8        
[37] stringi_0.5-5        grid_3.2.1           tools_3.2.1         
[40] 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       
[46] futile.options_1.0.0 MASS_7.3-43          rpart_4.1-10        
[49] nnet_7.3-10

 

 

Thank you in advance,

A. Romney

ADD COMMENTlink written 2.4 years ago by arom20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 334 users visited in the last hour