Question: When should I use betaprior=T
0
gravatar for andrebolerbarros
5 months ago by
andrebolerbarros10 wrote:

Hi everyone,

I have RNASeq Data, with 4 conditions, 2 replicates each (very far from ideal, I know). By looking at my data through heatmap and PCA, I see that there are relevant differences within conditions, among replicates.

To further analyze this dataset, I got the recommendation of using betaPrior=TRUE instead of the default FALSE. What I would like to know is if there's any scenario where using this option is more recommendable than following the standard pipeline (betaPrior=FALSE w/ lfcshrink).

Thanks!

deseq2 • 115 views
ADD COMMENTlink modified 5 months ago by Michael Love23k • written 5 months ago by andrebolerbarros10
Answer: When should I use betaprior=T
0
gravatar for Michael Love
5 months ago by
Michael Love23k
United States
Michael Love23k wrote:

Not really a use case. It’s obsolete except we kept it to not break old code that used it. The apeglm paper shows that the new heavy tailed methods (apeglm and ashr) outperform the Normal prior pretty much in every case.

ADD COMMENTlink written 5 months ago by Michael Love23k
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