Hey,

I am analyzing a proteomics dataset with 3 conditions and a total of 10 samples (columns) and 9650 proteins (rows). I want to apply VSN to my data table for normalization, but I got this error message: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'

I was checking whether my data contains infinite values or if all values in one column are the same, but this is not the case.

Can someone help me and tell me why vsn cannot run with this specific dataset and what I can do? (This is like the 20th proteomics data set that I am trying to normalize for my thesis and never had this problem before)

norm_dt <- justvsn(as.matrix(dt))

Error that I get:

vsn2: 9650 x 10 matrix (1 stratum). 
Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'

Some details about by session (I am building a complete workflow therefore I am not posting my whole sessionInfo() here)

• R version 4.2.2
• vsn version 3.66.0

If someone needs the data to check what the problem is, I can send it:)