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 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?