Question

DESeq2 lfc shrinkage

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6.3 years ago

rthapa ▴ 90

Hi! How can we determine the coefficient value while applying lfcShrink() with the coefficient argument? Thanks

rna-seq • 1.7k views

ADD COMMENT • link updated 4.9 years ago by lshepard ▴ 470 • written 6.3 years ago by rthapa ▴ 90

score 0 · Answer 1 · 2019-06-03

It has been a while but I just saw this. To not leave it unanswered in case others come across this: check the potential coefficients from using the function resultsNames(dds) [dds: object name to DESeqDataSet]

Further, check the section of the vignette called "Note on factor levels", to change the reference group if needed.