DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
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gdolsten • 0
@bf72196f
Last seen 1 day ago
United States
cells <- dba(sampleSheet = samples)
cells <- dba.count(cells, summits=FALSE)
cells <- dba.normalize(cells)
cells <- dba.contrast(cells)
cells <- dba.analyze(cells)
diffbind_deseq <- dba.analyze(cells, bRetrieveAnalysis=TRUE)
diffbind_res = results(diffbind_deseq, contrast=c("Tissue", "cell1", "cell2"))

report <- dba.report(cells, th=1)

Then, when I print report, and when I print diffbind_res[order(diffbind_res$padj), ], I get different results. For example, I get a Fold of 3.97436 in report, but a log2FoldChange of -4.02610 in diffbind_res, while the p-values and FDRs match exactly. What is the reason for this discrepancy?

DESeq2 Diffbind • 70 views
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Rory Stark ★ 4.0k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

DiffBind uses the capabilities built into DESeq2 to "shrink" the fold changes by applying DESeq2::lfcShrink() (with the apeglm estimator) to the report obtained from DESeq2::results(). Have a look at the help page for lfcShrink().

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