Question: 'DESeqDataSetFromTximport' not found
gravatar for zhizhon
11 months ago by
zhizhon0 wrote:


I installed DESeq2,  and it can be loaded normally. But there is no  "DESeqDataSetFromTximport".

I googled the error message, unfortunately no satisfying answer exists. So anyone here know what is the problem?

> DESeq
DESeq                       DESeqDataSetFromHTSeqCount  DESeqResults                DESeq2::
DESeqDataSet                DESeqDataSetFromMatrix      DESeqTransform

Thanks for any answer!


ADD COMMENTlink written 11 months ago by zhizhon0
gravatar for Guido Hooiveld
11 months ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

Please provide the output of sessionInfo()! The fuction is (at least) available when using R-3.4.x and Bioconductor v3.5. This will run DESeq2 v1.16.1, which thus contains the function DESeqDataSetFromTximport. See below for my SessionInfo().

<<edit>> The DESeq2 news file states that from v1.12.0 onwards  DESeqDataSetFromTximport has been added to DESeq2. You likely are thus using a very old version... Solution: update R and Bioconductor to its latest versions.


> sessionInfo()
R version 3.4.2 Patched (2017-10-09 r73515)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DESeq2_1.16.1              SummarizedExperiment_1.6.5
 [3] DelayedArray_0.2.7         matrixStats_0.52.2        
 [5] Biobase_2.36.2             GenomicRanges_1.28.6      
 [7] GenomeInfoDb_1.12.3        IRanges_2.10.5            
 [9] S4Vectors_0.14.7           BiocGenerics_0.22.1       
[11] BiocInstaller_1.26.1      

loaded via a namespace (and not attached):
 [1] genefilter_1.58.1       locfit_1.5-9.1          splines_3.4.2          
 [4] lattice_0.20-35         colorspace_1.3-2        htmltools_0.3.6        
 [7] base64enc_0.1-3         blob_1.1.0              survival_2.41-3        
[10] XML_3.98-1.9            rlang_0.1.2             DBI_0.7                
[13] foreign_0.8-69          BiocParallel_1.10.1     bit64_0.9-7            
[16] RColorBrewer_1.1-2      GenomeInfoDbData_0.99.0 plyr_1.8.4             
[19] stringr_1.2.0           zlibbioc_1.22.0         munsell_0.4.3          
[22] gtable_0.2.0            htmlwidgets_0.9         memoise_1.1.0          
[25] latticeExtra_0.6-28     knitr_1.17              geneplotter_1.54.0     
[28] AnnotationDbi_1.38.2    htmlTable_1.9           Rcpp_0.12.13           
[31] acepack_1.4.1           xtable_1.8-2            scales_0.5.0           
[34] backports_1.1.1         checkmate_1.8.5         Hmisc_4.0-3            
[37] annotate_1.54.0         XVector_0.16.0          bit_1.1-12             
[40] gridExtra_2.3           ggplot2_2.2.1           digest_0.6.12          
[43] stringi_1.1.5           grid_3.4.2              tools_3.4.2            
[46] bitops_1.0-6            magrittr_1.5            RSQLite_2.0            
[49] lazyeval_0.2.1          RCurl_1.95-4.8          tibble_1.3.4           
[52] Formula_1.2-2           cluster_2.0.6           Matrix_1.2-11          
[55] data.table_1.10.4-3     rpart_4.1-11            nnet_7.3-12            
[58] compiler_3.4.2         


ADD COMMENTlink modified 11 months ago • written 11 months ago by Guido Hooiveld2.3k
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