Possibly bug in newSeqExpressionSet function
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jens • 0
@jens-20467
Last seen 2.5 years ago

Hi,

I have encountered an unexpected behaviour of the newSeqExpressionSet function. Passing an integer count matrix 'count.m' of size 4957x999 to the function results in the following error:

> newSeqExpressionSet(count.m)
Error in validObject(.Object) : 
  invalid class “SeqExpressionSet” object: featureNames differ between assayData and featureData

Using the same matrix works if the dimensionality is specified explicitly:

> newSeqExpressionSet(count.m[1:4957,1:999])
SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 4957 features, 999 samples 
  element names: counts, normalizedCounts, offset 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  

The abstract form also works as expected:

> newSeqExpressionSet(count.m[1:dim(count.m)[1],1:dim(count.m)[2]])
SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 4957 features, 999 samples 
  element names: counts, normalizedCounts, offset 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  

Software versions:

R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Biobase_2.42.0

Although providing the explicit dimension values is a fairly simple work-around, it seems to be a bug worth fixing.

I would share the input matrix if required for validation.

Kind regards, Jens

software error EDASeq • 385 views
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In the future please add the package that the function comes from as a post tag. Please also include the full sessionInfo() that show the versions of the packages you are using. Your versions information you provide does not include the package the function came from.

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Thanks for the suggestions. I have reproduced the error on a second computer (my laptop) today and the full sessionInfo() is below.

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
 [1] gplots_3.0.1.1              ggplot2_3.1.0              
 [3] biomaRt_2.38.0              DESeq2_1.22.2              
 [5] RUVSeq_1.16.1               edgeR_3.24.3               
 [7] EDASeq_2.16.3               ShortRead_1.40.0           
 [9] GenomicAlignments_1.18.1    Rsamtools_1.34.1           
[11] Biostrings_2.50.2           XVector_0.22.0             
[13] ExpressionAtlas_1.10.0      xml2_1.2.0                 
[15] limma_3.38.3                SummarizedExperiment_1.12.0
[17] DelayedArray_0.8.0          matrixStats_0.54.0         
[19] GenomicRanges_1.34.0        GenomeInfoDb_1.18.2        
[21] IRanges_2.16.0              S4Vectors_0.20.1           
[23] Biobase_2.42.0              BiocGenerics_0.28.0        
[25] BiocParallel_1.16.6        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           bit64_0.9-7            RColorBrewer_1.1-2    
 [4] progress_1.2.0         httr_1.4.0             backports_1.1.3       
 [7] tools_3.5.3            R6_2.4.0               KernSmooth_2.23-15    
[10] rpart_4.1-13           Hmisc_4.2-0            DBI_1.0.0             
[13] lazyeval_0.2.2         colorspace_1.4-1       nnet_7.3-12           
[16] withr_2.1.2            tidyselect_0.2.5       gridExtra_2.3         
[19] prettyunits_1.0.2      bit_1.1-14             compiler_3.5.3        
[22] htmlTable_1.13.1       rtracklayer_1.42.2     caTools_1.17.1.2      
[25] checkmate_1.9.1        scales_1.0.0           genefilter_1.64.0     
[28] DESeq_1.34.1           stringr_1.4.0          digest_0.6.18         
[31] foreign_0.8-71         R.utils_2.8.0          htmltools_0.3.6       
[34] base64enc_0.1-3        pkgconfig_2.0.2        htmlwidgets_1.3       
[37] rlang_0.3.3            rstudioapi_0.10        RSQLite_2.1.1         
[40] hwriter_1.3.2          gtools_3.8.1           acepack_1.4.1         
[43] dplyr_0.8.0.1          R.oo_1.22.0            RCurl_1.95-4.12       
[46] magrittr_1.5           GenomeInfoDbData_1.2.0 Formula_1.2-3         
[49] Matrix_1.2-17          Rcpp_1.0.1             munsell_0.5.0         
[52] R.methodsS3_1.7.1      stringi_1.4.3          MASS_7.3-51.3         
[55] zlibbioc_1.28.0        plyr_1.8.4             grid_3.5.3            
[58] blob_1.1.1             gdata_2.18.0           crayon_1.3.4          
[61] lattice_0.20-38        splines_3.5.3          GenomicFeatures_1.34.7
[64] annotate_1.60.1        hms_0.4.2              locfit_1.5-9.1        
[67] knitr_1.22             pillar_1.3.1           geneplotter_1.60.0    
[70] XML_3.98-1.19          glue_1.3.1             latticeExtra_0.6-28   
[73] data.table_1.12.0      gtable_0.3.0           purrr_0.3.2           
[76] assertthat_0.2.1       xfun_0.6               aroma.light_3.12.0    
[79] xtable_1.8-3           survival_2.44-1.1      tibble_2.1.1          
[82] AnnotationDbi_1.44.0   memoise_1.1.0          cluster_2.0.7-1       
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Reproduced on second computer with latest Biobase packages.

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