need help

[madhu9]

Hi,
I am exploring the vicar package for batch correction.
I wanted to know, is there is a way to export batch-corrected matrix as output.

Thanks

[dcgerard]

Hey @madhu9,

Thanks for your interest in vicar!

vicar will return the estimated confounders (the object Zhat in the returned list). It is generally recommended that you do any analysis jointly with Zhat rather than first subtracting off the effect due to Zhat. This is because if you export a batch-corrected matrix and then proceed with your analysis, then you are effectively assuming that any observed covariates are independent of the unobserved confounders, which can be a bad assumption. This is why vicar does not export such a matrix by default.

As long as you are doing a differential expression analysis and you are only interested in one covariate, then vicar will do this entire analysis for you.

But you can obtain a "batch-corrected" matrix via:

Ynew <- Y - mout$Zhat %*% mout$alphahat

Where Y is the matrix of responses. (Again, I would generally not recommend this)