Question

voom command broken in limma_3.34.5?

0

Entering edit mode

sjk314 • 0

@sjk314-14760

Last seen 6.3 years ago

Hello,

When I run

voom(counts_table, design_table, plot = TRUE)

I get

Error in voom(counts_table, design_table, plot = TRUE) :

  unused arguments (design = NULL, plot = TRUE)"

This is not congruent with the variables given in the vignette. I also tried using a DGEList object for the counts and I got the same error. My design and counts table work when I run the commands for limma-trend. My design table looks like:

            treatment control
RNA1HrTreatA    1    0
RNA1HrTreatB    1    0
RNA1HrCtrlA   0    1
RNA1HrCtrlB   0    1

My counts table is just a matrix of integers. If I make the plot command FALSE then I get the same error. If I remove the plot and design variable I get

Error in round(counts) : non-numeric argument to mathematical function

Is it possible that there is a bug in limma 3.34.5?

Session info ----------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.3 (2017-11-30)
 system   x86_64, darwin15.6.0        
 ui       RStudio (1.0.136)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2018-01-11                  

Packages --------------------------------------------------------------------------------------------------------------------------
 package              * version   date       source                            
 acepack                1.4.1     2016-10-29 CRAN (R 3.4.0)                    
 annotate               1.56.1    2017-11-13 Bioconductor                      
 AnnotationDbi          1.40.0    2017-10-31 Bioconductor                      
 assertthat             0.2.0     2017-04-11 CRAN (R 3.4.0)                    
 backports              1.1.2     2017-12-13 CRAN (R 3.4.3)                    
 base                 * 3.4.3     2017-12-07 local                             
 base64enc              0.1-3     2015-07-28 CRAN (R 3.4.0)                    
 bindr                  0.1       2016-11-13 cran (@0.1)                       
 bindrcpp             * 0.2       2017-06-17 cran (@0.2)                       
 Biobase              * 2.38.0    2017-10-31 Bioconductor                      
 BiocGenerics         * 0.24.0    2017-10-31 Bioconductor                      
 BiocInstaller        * 1.28.0    2017-10-31 Bioconductor                      
 BiocParallel           1.12.0    2017-10-31 Bioconductor                      
 biomaRt              * 2.34.1    2017-12-15 Bioconductor                      
 bit                    1.1-12    2014-04-09 CRAN (R 3.4.0)                    
 bit64                  0.9-7     2017-05-08 CRAN (R 3.4.0)                    
 bitops                 1.0-6     2013-08-17 CRAN (R 3.4.0)                    
 blob                   1.1.0     2017-06-17 CRAN (R 3.4.0)                    
 checkmate              1.8.5     2017-10-24 CRAN (R 3.4.2)                    
 cluster                2.0.6     2017-03-10 CRAN (R 3.4.3)                    
 colorspace             1.3-2     2016-12-14 CRAN (R 3.4.0)                    
 compiler               3.4.3     2017-12-07 local                             
 curl                   3.1       2017-12-12 CRAN (R 3.4.3)                    
 data.table             1.10.4-3  2017-10-27 CRAN (R 3.4.2)                    
 datasets             * 3.4.3     2017-12-07 local                             
 DBI                    0.7       2017-06-18 CRAN (R 3.4.0)                    
 DelayedArray         * 0.4.1     2017-11-07 Bioconductor                      
 DESeq2               * 1.18.1    2017-11-12 Bioconductor                      
 devtools             * 1.13.4    2017-11-09 CRAN (R 3.4.2)                    
 digest                 0.6.13    2017-12-14 CRAN (R 3.4.3)                    
 dplyr                * 0.7.4     2017-09-28 cran (@0.7.4)                     
 edgeR                * 3.20.6    2018-01-09 Bioconductor                      
 foreign                0.8-69    2017-06-22 CRAN (R 3.4.3)                    
 Formula                1.2-2     2017-07-10 CRAN (R 3.4.1)                    
 genefilter           * 1.60.0    2017-10-31 Bioconductor                      
 geneplotter            1.56.0    2017-10-31 Bioconductor                      
 GenomeInfoDb         * 1.14.0    2017-10-31 Bioconductor                      
 GenomeInfoDbData       1.0.0     2018-01-10 Bioconductor                      
 GenomicRanges        * 1.30.1    2017-12-21 Bioconductor                      
 ggplot2              * 2.2.1     2016-12-30 CRAN (R 3.4.0)                    
 glue                   1.2.0     2017-10-29 cran (@1.2.0)                     
 graphics             * 3.4.3     2017-12-07 local                             
 grDevices            * 3.4.3     2017-12-07 local                             
 grid                   3.4.3     2017-12-07 local                             
 gridExtra              2.3       2017-09-09 CRAN (R 3.4.1)                    
 gtable                 0.2.0     2016-02-26 CRAN (R 3.4.0)                    
 Hmisc                  4.1-0     2017-12-19 CRAN (R 3.4.3)                    
 htmlTable              1.11.1    2017-12-27 CRAN (R 3.4.3)                    
 htmltools              0.3.6     2017-04-28 CRAN (R 3.4.0)                    
 htmlwidgets            0.9       2017-07-10 CRAN (R 3.4.1)                    
 httr                   1.3.1     2017-08-20 CRAN (R 3.4.1)                    
 IRanges              * 2.12.0    2017-10-31 Bioconductor                      
 knitr                  1.18      2017-12-27 CRAN (R 3.4.3)                    
 labeling               0.3       2014-08-23 CRAN (R 3.4.0)                    
 lattice                0.20-35   2017-03-25 CRAN (R 3.4.3)                    
 latticeExtra           0.6-28    2016-02-09 CRAN (R 3.4.0)                    
 lazyeval               0.2.1     2017-10-29 CRAN (R 3.4.2)                    
 limma                * 3.34.5    2017-12-23 Bioconductor                      
 locfit                 1.5-9.1   2013-04-20 CRAN (R 3.4.0)                    
 magrittr               1.5       2014-11-22 CRAN (R 3.4.0)                    
 Matrix                 1.2-12    2017-11-20 CRAN (R 3.4.3)                    
 matrixStats          * 0.52.2    2017-04-14 CRAN (R 3.4.0)                    
 memoise                1.1.0     2017-04-21 CRAN (R 3.4.0)                    
 methods              * 3.4.3     2017-12-07 local                             
 munsell                0.4.3     2016-02-13 CRAN (R 3.4.0)                    
 nnet                   7.3-12    2016-02-02 CRAN (R 3.4.3)                    
 parallel             * 3.4.3     2017-12-07 local                             
 pillar                 1.0.1     2017-11-27 CRAN (R 3.4.3)                    
 pkgconfig              2.0.1     2017-03-21 CRAN (R 3.4.0)                    
 plyr                   1.8.4     2016-06-08 CRAN (R 3.4.0)                    
 prettyunits            1.0.2     2015-07-13 CRAN (R 3.4.0)                    
 progress               1.1.2     2016-12-14 CRAN (R 3.4.0)                    
 purrr                  0.2.4     2017-10-18 cran (@0.2.4)                     
 R6                     2.2.2     2017-06-17 CRAN (R 3.4.0)                    
 RColorBrewer           1.1-2     2014-12-07 CRAN (R 3.4.0)                    
 Rcpp                   0.12.14   2017-11-23 CRAN (R 3.4.3)                    
 RCurl                  1.95-4.10 2018-01-04 CRAN (R 3.4.3)                    
 reshape2             * 1.4.3     2017-12-11 CRAN (R 3.4.3)                    
 rhdf5                * 2.22.0    2017-10-31 Bioconductor                      
 rlang                  0.1.6     2017-12-21 CRAN (R 3.4.3)                    
 rpart                  4.1-11    2017-03-13 CRAN (R 3.4.3)                    
 RSQLite                2.0       2017-06-19 CRAN (R 3.4.1)                    
 rstudioapi             0.7       2017-09-07 CRAN (R 3.4.1)                    
 S4Vectors            * 0.16.0    2017-10-31 Bioconductor                      
 scales                 0.5.0     2017-08-24 CRAN (R 3.4.1)                    
 sleuth               * 0.29.0    2018-01-10 Github (pachterlab/sleuth@8308dfd)
 splines                3.4.3     2017-12-07 local                             
 stats                * 3.4.3     2017-12-07 local                             
 stats4               * 3.4.3     2017-12-07 local                             
 stringi                1.1.6     2017-11-17 CRAN (R 3.4.2)                    
 stringr              * 1.2.0     2017-02-18 CRAN (R 3.4.0)                    
 SummarizedExperiment * 1.8.1     2017-12-19 Bioconductor                      
 survival               2.41-3    2017-04-04 CRAN (R 3.4.3)                    
 tibble                 1.4.1     2017-12-25 CRAN (R 3.4.3)                    
 tidyr                  0.7.2     2017-10-16 cran (@0.7.2)                     
 tidyselect             0.2.3     2017-11-06 cran (@0.2.3)                     
 tools                  3.4.3     2017-12-07 local                             
 tximport             * 1.6.0     2017-10-31 Bioconductor                      
 utils                * 3.4.3     2017-12-07 local                             
 withr                  2.1.1     2017-12-19 CRAN (R 3.4.3)                    
 XML                    3.98-1.9  2017-06-19 CRAN (R 3.4.1)                    
 xtable                 1.8-2     2016-02-05 CRAN (R 3.4.0)                    
 XVector                0.18.0    2017-10-31 Bioconductor                      
 zlibbioc               1.24.0    2017-10-31 Bioconductor

limma voom • 1.2k views

ADD COMMENT • link updated 6.3 years ago by Gordon Smyth 50k • written 6.3 years ago by sjk314 • 0

score 1 · Answer 1 · 2018-01-11

1

Entering edit mode

Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 14 months ago

United States

The Error in round(counts) : non-numeric argument to mathematical function you are getting suggests that your counts object isn't what you think it is.

What is the output of class(counts) and class(counts[1])?

ADD COMMENT • link 6.3 years ago Steve Lianoglou ★ 13k

score 1 · Answer 2 · 2018-01-11

1

Entering edit mode

Aaron Lun ★ 28k

@alun

Last seen 15 hours ago

The city by the bay

Are you sure you're calling limma::voom? The function shouldn't even call round.

ADD COMMENT • link 6.3 years ago Aaron Lun ★ 28k

score 0 · Answer 3 · 2018-01-11

No, there isn't a bug in voom() in limma 3.34.5. The fact that the error messages you have are not compatible with the voom function in limma strongly suggests that you are not calling limma's voom() function at all. It would seem that you must have another "voom" function in your search path that is over-writing the one in the limma package. This could be a function that you have created or it could be function in one of the packages you have loaded.

You could run

limma::voom(counts_table, design_table, plot = TRUE)

to make sure you're getting the limma function.

Or else, start a clean R session and load limma by itself. You don't need the enormous number of packages you currently have loaded to run voom.

You can BTW just type

voom

at the prompt to see which function you're using. If the last line doesn't say <environment: namespace:limma>, then you're not using the limma function.