I am working with 88 samples. To remove batch effect from the samples I am trying to use SVA package. But when I am trying to estimate number of latent factors. I can see in the tutorial and other questions on different forums, the number of surrogate variables is really small. But I am estimating surrogate number - 83. When I am changing method from "leek" to "be" the number goes down to 1. When I try to estimate surrogate variables, it doesn't work.
I am not sure if these numbers are dependable or I am doing something wrong. Can somebody help me?
Thanks in advance