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Question: voom command broken in limma_3.34.5?
0
gravatar for sjk314
4 days ago by
sjk3140
sjk3140 wrote:

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                  

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ADD COMMENTlink modified 4 days ago by Gordon Smyth32k • written 4 days ago by sjk3140
1
gravatar for Steve Lianoglou
4 days ago by
Genentech
Steve Lianoglou12k wrote:

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 COMMENTlink written 4 days ago by Steve Lianoglou12k
1
gravatar for Aaron Lun
4 days ago by
Aaron Lun18k
Cambridge, United Kingdom
Aaron Lun18k wrote:

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

ADD COMMENTlink modified 4 days ago • written 4 days ago by Aaron Lun18k
0
gravatar for Gordon Smyth
4 days ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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.

 

ADD COMMENTlink modified 4 days ago • written 4 days ago by Gordon Smyth32k
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