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Question: 'DESeqDataSetFromTximport' not found
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gravatar for zhizhon
20 days ago by
zhizhon0
zhizhon0 wrote:

Hello,

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!

zhong

ADD COMMENTlink written 20 days ago by zhizhon0
0
gravatar for Guido Hooiveld
20 days ago by
Guido Hooiveld2.1k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.1k 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

locale:
[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 20 days ago • written 20 days ago by Guido Hooiveld2.1k
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