[BioC] Back-estimating batch variables from SVA for ComBat?

Hollis Wright wrighth at ohsu.edu
Mon Aug 6 23:50:03 CEST 2012

Hi, all; we're working with some gene expression data and we suspect that there may be some irregularities in arrays; unfortunately, these arrays were run some time ago and we're not actually sure what the batches (if any) they were run in were at this point; complicating matters, this is also a timepoint analysis so there's some technical variability there most likely. Long-run, we'd like to run WGCNA and some similar methods on this data and I'd had good luck with ComBat adjusting for batches in a previous case where we did have that information. Is there any way to use sva estimates to estimate what the batches "should" be for our data? sva does estimate and find three significant latent variables but I'm not sure what (if anything) can be done from there in terms of adjusting the expression levels to compensate for the latent variables; obviously we'd also be concerned about losing the biological variability if we make any adjustments. Is this possible, or am I heading in the wrong direction here?

Hollis Wright, PhD
Ojeda Lab, Division of Neuroscience
Oregon Health and Science University

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