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 with
contrast, or add
coefin the
resultsNames`?