DESeq2: Error: could not find function "vst"
2
0
Entering edit mode
charlesh • 0
@charlesh-13279
Last seen 5.5 years ago

Hi

A student was working thru the airway tutorial for DESeq2, and got the following error:

> vsd <- vst(dds, blind = FALSE)

Error: could not find function "vst"

According to  sessionInfo() we have installed: DESeq2_1.10.1

Any suggestions?

Charles

> sessionInfo()

R version 3.2.0 (2015-04-16)

Platform: x86_64-unknown-linux-gnu (64-bit)

Running under: Ubuntu 14.04.5 LTS

 

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] hexbin_1.27.1              vsn_3.38.0                

 [3] DESeq2_1.10.1              RcppArmadillo_0.7.900.2.0 

 [5] Rcpp_0.12.11               magrittr_1.5              

 [7] BiocParallel_1.4.3         GenomicAlignments_1.6.3   

 [9] GenomicFeatures_1.22.13    AnnotationDbi_1.32.3      

[11] Rsamtools_1.22.0           Biostrings_2.38.4         

[13] XVector_0.10.0             airway_0.104.0            

[15] SummarizedExperiment_1.0.2 Biobase_2.30.0            

[17] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        

[19] IRanges_2.4.8              S4Vectors_0.8.11          

[21] BiocGenerics_0.16.1        rmarkdown_1.6             

[23] knitr_1.16                 BiocStyle_1.8.0           

 

loaded via a namespace (and not attached):

 [1] splines_3.2.0         Formula_1.2-1         affy_1.48.0          

 [4] latticeExtra_0.6-28   RSQLite_1.1-2         backports_1.1.0      

 [7] lattice_0.20-35       limma_3.26.9          digest_0.6.12        

[10] RColorBrewer_1.1-2    checkmate_1.8.2       colorspace_1.3-2     

[13] preprocessCore_1.32.0 htmltools_0.3.6       Matrix_1.2-10        

[16] plyr_1.8.4            XML_3.98-1.8          biomaRt_2.26.1       

[19] genefilter_1.52.1     zlibbioc_1.16.0       xtable_1.8-2         

[22] scales_0.4.1          affyio_1.40.0         htmlTable_1.9        

[25] tibble_1.3.3          annotate_1.48.0       ggplot2_2.2.1        

[28] nnet_7.3-12           lazyeval_0.2.0        survival_2.41-3      

[31] memoise_1.1.0         evaluate_0.10         foreign_0.8-68       

[34] BiocInstaller_1.20.3  tools_3.2.0           data.table_1.10.4    

[37] stringr_1.2.0         munsell_0.4.3         locfit_1.5-9.1       

[40] cluster_2.0.6         lambda.r_1.1.9        rlang_0.1.1          

[43] futile.logger_1.4.3   grid_3.2.0            RCurl_1.95-4.8       

[46] htmlwidgets_0.8       labeling_0.3          bitops_1.0-6         

[49] base64enc_0.1-3       gtable_0.2.0          DBI_0.6-1            

[52] gridExtra_2.2.1       rtracklayer_1.30.4    Hmisc_4.0-3          

[55] rprojroot_1.2         futile.options_1.0.0  stringi_1.1.5        

[58] geneplotter_1.48.0    rpart_4.1-11          acepack_1.4.1        

deseq2 • 2.1k views
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2
Entering edit mode
@laurent-gatto-5645
Last seen 11 weeks ago
Belgium

You need to update your version of R (current version is 3.4, you are still using 3.2), which will get you the latest version of DESeq2 (v 1.16.0, you have 1.10.1) and vst, which was introduced in version 1.12.0.

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0
Entering edit mode
charlesh • 0
@charlesh-13279
Last seen 5.5 years ago

OK, great - thanks!

Charles

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