Batch effect problem using SVA showing problems
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amoltej ▴ 10
@amoltej-7192
Last seen 4.0 years ago
Australia

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

SVA combat sva batch effect • 721 views
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Jeff Leek ▴ 610
@jeff-leek-5015
Last seen 7 months ago
United States

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

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Hello, Thanx for the reply. May I know reason behind it? and how the big number for the latent factors is wrong?

 

Thanx

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