[Warning] Number of genes in parameter num.genes.kept is largen than the number of mean values

[Cem-Gulec]

[KatharinaSchmid]

This is a correct warning message. The num.genes.kept parameter removes genes that have only zero counts (e.g. if you have a matrix with 50,000 genes but only 18,000 genes have a value larger than 0 it costs unnecessary runtime & memory to keep all 50,000 genes throughout the processing. In your case, however, your complete matrix has only 19,492 entries. So you can’t keep 21,000 genes, if you don’t have that many genes. The warning message tells you that it keeps instead all available genes, i.e. 19,492. I hope this explanation helps.