Entering edit mode
5.0 years ago
rrbutleriii
▴
260
I am doing a time series analysis on a single cell line as in Section 9 of the RNA-Seq workflow guide and was wondering if it is possible or advisable to apply lfc shrinkage to the result.
library("fission")
data("fission")
ddsTC <- DESeqDataSet(fission, ~ strain + minute + strain:minute)
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ strain + minute)
resTC <- results(ddsTC)
resTC.ape <- lfcShrink(ddsTC, type = "apeglm")
This errors at the last step as I am unsure what to put for coef =
. The possible names are the pairwise comparisons of the time points instead of a comparison to baseline:
> resultsNames(ddsTC)
[1] "Intercept" "strain_mut_vs_wt" "minute_15_vs_0" "minute_30_vs_0"
[5] "minute_60_vs_0" "minute_120_vs_0" "minute_180_vs_0" "strainmut.minute15"
[9] "strainmut.minute30" "strainmut.minute60" "strainmut.minute120" "strainmut.minute180"