Batch effect correction
Entering edit mode
3.4 years ago

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.

sva combat matlab • 1.2k views
Entering edit mode
3.4 years ago

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

Login before adding your answer.

Traffic: 1850 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6