Question: getting DiffBind full result list
0
gravatar for rafael.munoz.viana
10 months ago by
rafael.munoz.viana0 wrote:

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

chipseq diffbind deseq2 • 211 views
ADD COMMENTlink modified 10 months ago by Rory Stark2.8k • written 10 months ago by rafael.munoz.viana0
Answer: getting DiffBind full result list
1
gravatar for Rory Stark
10 months ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k wrote:

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).

 

ADD COMMENTlink written 10 months ago by Rory Stark2.8k
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