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Question: DESeq2 LFC shrinkage is for designs with interactions
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gravatar for yk.gatc
5 days ago by
yk.gatc0
yk.gatc0 wrote:

Hi,

It seems like LFC shrinkage is not implemented for designs with interactions. Is there a way to get shrinked LFC values for designs with interactions?

DESeq2_1.19.14

Thanks,

YK

ADD COMMENTlink modified 4 days ago • written 5 days ago by yk.gatc0

Thanks Michael for the quick response. 

I did try "ashr" method, but it gave me the following warning - 

> resultsNames(dds)
 [1] "Intercept"    "grp_Y_vs_X"   "grpX.ind.n10" "grpY.ind.n10" "grpX.ind.n2"
 [6] "grpY.ind.n2"  "grpX.ind.n3"  "grpY.ind.n3"  "grpX.ind.n4"  "grpY.ind.n4"
[11] "grpX.ind.n5"  "grpY.ind.n5"  "grpX.ind.n6"  "grpY.ind.n6"  "grpX.ind.n7"
[16] "grpY.ind.n7"  "grpX.ind.n8"  "grpY.ind.n8"  "grpX.ind.n9"  "grpY.ind.n9"
[21] "grpX.cndT"    "grpY.cndT"
> res <- results(dds, contrast=list("grpY.cndT","grpX.cndT"))


> resLFC <- lfcShrink(dds,type="ashr", res=res)
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
Due to absence of package REBayes, switching to EM algorithm
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.

Any thoughts?

ADD REPLYlink modified 4 days ago • written 4 days ago by yk.gatc0

I moved your "Answer" to a "Comment".

I would recommend to use apeglm in this case.

ADD REPLYlink written 4 days ago by Michael Love15k
0
gravatar for Michael Love
4 days ago by
Michael Love15k
United States
Michael Love15k wrote:

If you check ?lfcShrink in current release it says,

     For ‘type="normal"’, shrinkage cannot be applied to coefficients
     in a model with interaction terms.

So for >= v1.18 with apeglm or ashr shrinkage estimators, you can perform this. We haven't written up a full explanation of these in the vignette, it has a section that I'm looking to expand, but haven't had the time yet. Here is some demo code though for an interaction term:

dds <- makeExampleDESeqDataSet()
dds$x <- factor(rep(1:2,6))
design(dds) <- ~x + condition + x:condition
dds <- DESeq(dds, quiet=TRUE)
resultsNames(dds)
[1] "Intercept"        "x_2_vs_1"         "condition_B_vs_A" "x2.conditionB"

​res1 <- lfcShrink(dds, coef=4, type="apeglm")
res2 <- lfcShrink(dds, coef=4, type="ashr")
ADD COMMENTlink written 4 days ago by Michael Love15k
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