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