In presence of missing data (for the input data), i can only retrieve the eigenvalues on the components selected by the user. In other words, I do not know the total variance of the data and thus cannot get the explained variance per component.
Kim-Anh Le Caorepo owner
This explains why we have different outputs when you run a PCA-missing values (via nipals) and a normal PCA.
For missing values, proceed as usual.
Dr. Kim-Anh Lê Cao
NHMRC Career Development Fellow
ResTeach Affiliate (School of Chemistry and Molecular Biosciences)