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.
1 answer
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:
- include
batchas a covariate in your design model (this will adjust the statistical values like any other covariate) - directly model batch and modify your raw counts prior to normalisation
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