plotRLE not working in scater
2
0
Entering edit mode
ian.oslo • 0
@ianoslo-13017
Last seen 5.4 years ago

I am following the scater workshop tutorial found here:

https://github.com/hemberg-lab/scRNA.seq.course/blob/master/13-exprs-norm.Rmd

I have run all of the code from the first 12 chapters without any problem.

When I try to run this section of code:

plotRLE(
    umi.qc[endog_genes, ], 
    exprs_mats = list(Raw = "log2_counts", CPM = "exprs"),
    exprs_logged = c(TRUE, TRUE),
    colour_by = "batch"
)

 

I get this error,

Error: could not find function "plotRLE"

To reproduce the error, i tried in a new session:

#############
library(scater, quietly = TRUE)

scater::newSCESet()
#Error in scater::newSCESet() :
#  Require at least one of exprsData, tpmData, fpkmData or countData arguments.

scater::plotRLE()

#Error: 'plotRLE' is not an exported object from 'namespace:scater'

################

even though plotRLE is listed as a function here:

http://bioconductor.org/packages/release/bioc/manuals/scater/man/scater.pdf

Any help or hints appreciated

 

Ian

 

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] scater_1.2.0        ggplot2_2.2.1       Biobase_2.34.0      BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10         vipor_0.4.5          plyr_1.8.4           zlibbioc_1.20.0      viridis_0.4.0        bitops_1.0-6         tools_3.3.2         
 [8] biomaRt_2.30.0       digest_0.6.12        rhdf5_2.18.0         lattice_0.20-35      RSQLite_1.1-2        memoise_1.1.0        tibble_1.3.0        
[15] gtable_0.2.0         viridisLite_0.2.0    shiny_1.0.3          DBI_0.6-1            beeswarm_0.2.3       gridExtra_2.2.1      stringr_1.2.0       
[22] dplyr_0.5.0          S4Vectors_0.12.2     IRanges_2.8.2        stats4_3.3.2         locfit_1.5-9.1       grid_3.3.2           shinydashboard_0.5.3
[29] data.table_1.10.4    R6_2.2.1             AnnotationDbi_1.36.2 XML_3.98-1.7         ggbeeswarm_0.5.3     limma_3.30.13        reshape2_1.4.2      
[36] magrittr_1.5         edgeR_3.16.5         matrixStats_0.52.2   scales_0.4.1         htmltools_0.3.6      tximport_1.2.0       assertthat_0.2.0    
[43] mime_0.5             xtable_1.8-2         colorspace_1.3-2     httpuv_1.3.3         stringi_1.1.5        RCurl_1.95-4.8       lazyeval_0.2.0      
[50] munsell_0.4.3        rjson_0.2.15  
software error scater plotRLE • 1.0k views
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1
Entering edit mode
Aaron Lun ★ 27k
@alun
Last seen 9 hours ago
The city by the bay

Your package versions are out of date. We are currently on scater version 1.4.0 and BioC 3.5, running on R 3.4.0. Upgrade your installation and plotRLE will be available.

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0
Entering edit mode
ian.oslo • 0
@ianoslo-13017
Last seen 5.4 years ago

Thanks, that solved it.

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