Question: Applying lfcShrink to a time series analysis
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gravatar for rrbutleriii
10 months ago by
rrbutleriii70
US, Chicago
rrbutleriii70 wrote:

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"
rna-seq deseq2 time-series • 293 views
ADD COMMENTlink written 10 months ago by rrbutleriii70
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