Could not shrink after adjusting factor level reference in DESeq2

Question

[jfo]

my two conditions are Keme and Latik, so I have condition_keme_vs_latik (based on dds). I want Latik to be the reference so:

res <- results(dds, lfcThreshold = lfc_cutoff, alpha = padj_cutoff, contrast = c("condition", "latik", "keme")

Now, to shrink the LFC:

resLFC <- lfcShrink(dds_out, coef="condition_keme_vs_latik", type="apeglm", res = res)

Error ensues:

Error in lfcShrink(dds, coef = "condition_keme_vs_latik", type = "apeglm", : 'coef' should specify same coefficient as in results 'res'

Of course, reversing the contrast to the original would allow me to proceed since the resultName shows "condition_keme_vs_latik", which coef expects. How do I run lfcShrink using my preferred factor levels?

[jfo]

Okay. Sorry. I found a link to "Note on factor levels". Silly me.

[ATpoint]

It would be great if you can add a short explanation of the error and the solution to the answer field since this is a fairly common error and others might benefit from it in the future.

Answer 1

[jfo]

Sorry about that.

The error shows up because of the factor levels (changed reference to latik from keme) and the lfcShrink needs the right value for the coef (which can be determined using resultsName). The correct value would be the original keme as reference, i.e., condition_keme_vs_latik.

To run lfcShrink using my preferred reference condition, change the reference before running DESeq() using

dds$condition <- relevel(dds$condition, ref = "latik")