I have a dataset I'm analysing with deseq2. For plotting the data in a volcano plot I'm trying to run lfcSrhink on a contrast which somehow doesn't show on the resultNames.

This is the results of this command

[1] "Intercept"   "design_D0_KO_low_vs_D0_KO_high"  "design_D0_WT_high_vs_D0_KO_high" "design_D0_WT_low_vs_D0_KO_high"

What can I do to run e.g. KO-low vs. WT-low?

I tried to usecontrasts like in the results command.

when I run this:

> resMA <- lfcShrink(ddsMat, coef="design_D0_KO_low_vs_D0_KO_high", type="apeglm")
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

it works.

But this command returns an error:

> resMA <- lfcShrink(ddsMat, contrast = c("design", "D0_KO_low", "D0_KO_high"), type="apeglm")
Error in lfcShrink(ddsMat, contrast = c("design", "D0_KO_low", "D0_KO_high"),  : 
  type='apeglm' shrinkage only for use with 'coef'

Is there a way to run lfcShrink withcontrast, or addcoefin theresultsNames`?

Assa,

did you have a look at http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#extended-section-on-shrinkage-estimators and the advice following "Although apeglm cannot be used with contrast, we note that many designs can be easily rearranged such that what was a contrast becomes its own coefficient." in particular?

Hope this helps, kind regards,

Wolfgang