Question: DESeq2 lfcShrink warning use ashr method
0
gravatar for MatthewP
11 days ago by
MatthewP0
China
MatthewP0 wrote:

Hello, my 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.

MA plot

res <- results(dds, contrast=c("Treatment", "Sh2", "Control"))
plotMA(res)

plotMa
Plot link

deseq2 • 71 views
ADD COMMENTlink modified 8 days ago • written 11 days ago by MatthewP0

Mike, we directed the user here, as we were unsure about this one. I personally had not seen that warning message before. https://www.biostars.org/p/397274/

ADD REPLYlink written 9 days ago by Kevin Blighe190
Answer: DESeq2 lfcShrink warning use ashr method
0
gravatar for Michael Love
10 days ago by
Michael Love25k
United States
Michael Love25k wrote:

I added the warning to your post...

Can you post an MA plot of the un-shrunk LFC?

res <- results(dds, contrast=c(...))
plotMA(res, ylim=c(-6,6))
ADD COMMENTlink written 10 days ago by Michael Love25k

Ok, added to post now.

ADD REPLYlink written 8 days ago by MatthewP0

It looks like it's not shrinking much, so maybe I'd go with a different method.

You can use:

res <- lfcShrink(dds, coef="treatment_Sh2_vs_Control", type="apeglm")

right?

ADD REPLYlink written 7 days ago by Michael Love25k

Yes yes apeglm work.

ADD REPLYlink written 7 days ago by MatthewP0
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