Hello everyone, 

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

In this case, I would trust method="be". method="leek" tends to work better when the sample size is smaller (20-30 samples or less). 

Best

Jeff