DESeq2 lfcShrink warning use ashr method.

Question

[MatthewP]

Code and warning

> 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.

This post already report this warning, however I totally don't know what they mean. I need to know can I ignore this warning, use the result as normal?

[ATpoint]

Given that this method is wrapped into lfcShrink I suggest you ask this at BioC so that Mike Love (the maintainer of DESeq2) can have a look. Ignoring this? For sure not, what makes you think you could ignore such a striking warning message?

[Kevin Blighe]

Also, when you post on Bioconductor, please post the link here so that Biostars users can follow through. I have not seen this warning message before, so, it will be good to have more information.

Answer 1

[MatthewP]

Post link to Bioconductor forum.