Question: Batch effect correction
gravatar for gstavropoulos1991
24 months ago by
gstavropoulos199110 wrote:

Dear all,

I want to correct for batch effects. I have two data sets, two similar diseases, measured at completely different time points. When I do PCA, I clearly see two groups; however, this shouldn't be the case since those two diseases are rather similar and therefore, that's a clear indication of batch effects.

The thing is that I'm just getting started with batch effect corrections and therefore, I'm not really familiar with how I should properly do the analysis step by step. Consequently, I would appreciate if someone could shed some light on how I should proceed.

By the way, I have already read the SVA paper by Leek et al. but I didn't really get into the topic or how I should proceed.

Thank you in advance.

Regards, George.

matlab combat sva • 774 views
ADD COMMENTlink written 24 months ago by gstavropoulos199110
gravatar for Kevin Blighe
24 months ago by
Kevin Blighe59k
Kevin Blighe59k wrote:

Presumably you have gene expression data? How did you process it? Why do you have a matlab tag for your question?

Generally there are 2 options that allow us to deal with batch:

  1. include batch as a covariate in your design model (this will adjust the statistical values like any other covariate)
  2. directly model batch and modify your raw counts prior to normalisation
ADD COMMENTlink modified 24 months ago • written 24 months ago by Kevin Blighe59k
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