getting DiffBind full result list
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@rafaelmunozviana-16038
Last seen 3.3 years ago

Dear Bioconducters

I am running ChIPseq analyses via DiffBind 2.2.12 using DESeq option.
As indicated in the vignette I run dba.analyze() and the extract the results with dba.report()

I obtain the GR of the peaks that are significative changed, but I wonder if it is possible to get the data (Fold and FDR) of those that show no appreciable change

Kind regards

deseq2 diffbind chipseq • 411 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 23 hours ago
CRUK, Cambridge, UK

You can get stats for all the peaks by setting th=1 in the call to dba.report().

It's worth noting that it is not necessarily the case that peaks with higher FDR values are not changing, rather that there is insufficient evidence to be confident that they did change (potentially due to e.g. inadequate power given the variance in binding values for that peak).