Question: DESeq2 lfcShrink warning use ashr method
11 days ago by
MatthewP • 0
MatthewP • 0 wrote:
lfcShrink function gives warning I don't understand, post on biostar link.
> resLFC_sh2 <- lfcShrink(dds, contrast=c("Treatment", "Sh2", "Control"), type="ashr") using 'ashr' for LFC shrinkage. If used in published research, please cite: Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2. https://doi.org/10.1093/biostatistics/kxw041 Warning message: In estimate_mixprop(data, g, prior, optmethod = optmethod, control = control, : Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.
res <- results(dds, contrast=c("Treatment", "Sh2", "Control")) plotMA(res)
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