sva output interpretation

Question

[elb]

Hi guys, is there someone who can explain me the meaning of the sva output as from the sva R library? In other words I run svobj = sva(edata,mod,mod0,n.sv=n.sv) as here https://www.bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf but it is not clear to me the meaning of the three outputs: pprob.gam, pprob.b and the estimated surrogate variables. Are these last coefficients? Or what? In the help they say: pprob.gam: "A vector of the posterior probabilities each gene is affected by heterogeneity" (which type of heterogeneity?) sv: "The estimated surrogate variables, one in each column" (?? coefficients?) pprob.b: "A vector of the posterior probabilities each gene is affected by mod" (by the batch effect?)

Thank you in advance

Answer 1

[Devon Ryan]

All you really care about is sv, the estimated surrogate variables, which you can add to the model matrix you use for DE. pprob.b can be used to determine how individual genes are affected by your design. The latent variables for pprob.gam are the surrogate variables, so that's giving you information about how individual genes are affected by confounding surrogate variables.