This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error at cemitool function to get expression data/CEMiTool

Hi,

I have prepared a .txt file of RMA-normalized microarray dataset with samples in the columns and gene IDs in the rows (30 samples and 7000 genes totally). Entering this code, generates an error as follows and I don't know why???

cem <- cemitool(my_file)
**Error in matrixStats::rowVars(expr, na.rm = TRUE) : 
  Argument 'x' must be of type logical, integer or numeric, not 'character'.**

Thanks for your help in advance.

cemitool
• 1,860 views • link
updated by pedrostrusso • pedrostrusso • written by Microuser • Microuser

1 answer

Hi @Microuser,

Please note that my_file must be a data.frame, not a file name. In case it is, it's hard to say just from the error message, but it seems your expression data is being interpreted as character. Try running this before the cemitool function:

my_file <- my_file %>% mutate_all(as.numeric)
• 0 views • link
written by pedrostrusso • pedrostrusso

Log in to answer this question.

More posts like this