I am trying to use NIPALS to impute my missing data for my MS proteomic block.
When I run the following command:
nipals(untargeted.ru, ncomp = 10, reconst = TRUE)
I get this error:
Error in ph.new/drop(sqrt(crossprod(ph.new))) : non-conformable arrays
untargeted.ru is my proteomic dataset; with 49 samples in rows, and 409 proteins in columns. The missing values are indicated by NA. There is a very high rate of missingness in the dataset - 8237 out of 20041 observations are NA. Is this too much missing data?