Question: Batch correction with uncertain biological variables
gravatar for vedran.franke
22 months ago by
vedran.franke0 wrote:

I am currently trying to analyze a set of expression experiments from different tissues.

Some of the expression profiles originate from knockout experiments, for which we expect to cause trans-differentiation.

The experiments suffer from strong batch affects which are unknown, but fortunately, not perfectly confounded with biological variables of interest.

I have tried using sva to find the unknown batch effects - which works, however, I have a sense that the procedure might also be removing biological variance. 

Namely, the problem arises when specifying the mod matrix argument. If I specify the mod argument as WT - T1, WT - T2 ... KO - T1, KO - T2 ...; sva finds the batch effects, which results in samples clustering by their corresponding biological variables. However, there is a chance that some of the KO samples actually behave like WT samples - e.g. KO - T1 biologically becomes WT - T2, in which case sva actually removes the difference.

Is there a way to incorporate this uncertainty during sva modelling?

Additionally, I have found sva to be extremely sensitive to the exact samples which I use for estimating batch effects. Is there an easy way to assess the robustness of the bach effect estimation?


Best regards, 




ADD COMMENTlink written 22 months ago by vedran.franke0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 294 users visited in the last hour