Question: type='apeglm' shrinkage only for use with 'coef'
0
gravatar for wuyingncu
22 days ago by
wuyingncu0
China, Guangzhou
wuyingncu0 wrote:
dd2 <- lfcShrink(dds, contrast=contrast, res=dd1)
Error in lfcShrink(dds, contrast = contrast, res = dd1) : 
  type='apeglm' shrinkage only for use with 'coef'

Does anybody know how to explain this? It's stuck on me for a long time!!!!

rna-seq R • 192 views
ADD COMMENTlink modified 22 days ago by genomax87k • written 22 days ago by wuyingncu0
  1. contrast <- c("sample", "normal", "cancer")
  2. dd2 <- lfcShrink(dds, contrast=contrast, res=dd1)

thanks, but I don't know why

The error messageļ¼š Error in lfcShrink(dds, contrast = contrast, res = dd1) : type='apeglm' shrinkage only for use with 'coef'

ADD REPLYlink modified 22 days ago • written 22 days ago by wuyingncu0

Use ADD REPLY/ADD COMMENT when responding to existing messages to keep threads logically organized.

ADD REPLYlink written 22 days ago by genomax87k

Is dd1 one of the members of resultsNames(dds) as required ?

ADD REPLYlink written 22 days ago by jomo018610
1
gravatar for Devon Ryan
22 days ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

Set type to something else, such as normal or ashr.

ADD COMMENTlink written 22 days ago by Devon Ryan96k

The DESeq2 vignette has a table summarizing the different types ("Extended section on shrinkage estimators" section).

ADD REPLYlink written 22 days ago by igor11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1083 users visited in the last hour