MA plot of shrunken fold change

Question

[Sudip]

resimm1_LFC <- lfcShrink(dds_condition, coef="condition_imm1Ta_0_vs_WT_0", type="apeglm")
plotMA(resimm1_LFC, ylim=c(-2,2),main="MA plot of WT vs imm1Ta")

I am trying to do a MA plot but I do not see this coefficient condition_imm1Ta_0_vs_WT_0 when I do resultsName(dds_condition). Why is this?

Answer 1

[ATpoint]

You will need to relevel to make all comparisons available as coefficients, see type='apeglm' shrinkage only for use with 'coef', or just use ashr shrinkage and call it a day.

[Sudip]

Thank you.