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Question: diffbind finding not differential site
0
gravatar for woongjaej
3 months ago by
woongjaej0
Korea/Seoul/Yonsei University, College of Medicine
woongjaej0 wrote:

Hi,

 

I'm using Diffbind to analysis differential binding H3K27Ac histone ChIP-seq site!

I'm curious whether I can find all the relative site like not differentially binded site in both conditions, up binding in condition1 and, up binding in condition2.

I gave the fold value 0 in dba.analyze, but the result give me just about | 0.3 fold | differentially binded sites.

 

Any suggestion will be very grateful!.

 

Thanks,

 

Woongjae

ADD COMMENTlink modified 3 months ago by Rory Stark2.7k • written 3 months ago by woongjaej0
Answer: diffbind finding not differential site
3
gravatar for Rory Stark
3 months ago by
Rory Stark2.7k
CRUK, Cambridge, UK
Rory Stark2.7k wrote:

The null hypothesis in these tests is that the site did not change binding affinity. Low p-value/FDR value indicate confidence that this is no true -- that there is a change. Higher p-value/FDR values,on the other hand, do not indicate confidence that the sites did not change, only that there is not sufficient evidence to be confident that a change occurred. Bottom line: this tool can not be used to test for unchanged site.

If you want to see sites with low fold-changes, you should set th=1 in the call to dba.report() to retrieve all the binding sites. Then you can filter by low Fold changes and higher FDR. You can then sort to see the lowest fold changes first. Here's an example:

data(tamoxifen_analysis)
rep <- dba.report(tamoxifen,th=1)
filter <- abs(rep$Fold)<1 & rep$FDR>.1
lowfold <- rep[filter,]
lowfold[order(abs(lowfold$Fold),decreasing=FALSE),]

 

ADD COMMENTlink written 3 months ago by Rory Stark2.7k

Thanks Rory!! This is very helpful solution!

Woongjae

ADD REPLYlink written 3 months ago by woongjaej0
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