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Question: DESeq2: Error: could not find function "vst"
0
gravatar for charlesh
8 weeks ago by
charlesh0
charlesh0 wrote:

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        

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by charlesh0
2
gravatar for Laurent Gatto
8 weeks ago by
Laurent Gatto820
United Kingdom
Laurent Gatto820 wrote:

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.

ADD COMMENTlink written 8 weeks ago by Laurent Gatto820
0
gravatar for charlesh
8 weeks ago by
charlesh0
charlesh0 wrote:

OK, great - thanks!

Charles

ADD COMMENTlink written 8 weeks ago by charlesh0
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