R's DiffBind. Error in pv.DBAplotVolcano(DBA, contrast = contrast, method = method,: object 'sigSites' not found
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Entering edit mode
2.3 years ago
msimmer92 ▴ 290

Hello all, I am using R´s DiffBind to find differentially bound sites on my ChIP-seq data. I have ¨healthy¨ condition, and two other ¨unhealthy¨ conditions that I want to compare. When I compare one unhealthy to the healthy, it all works fine with my script. I get nice volcano and MA plots (which is what I want, in this case):

results=dba(sampleSheet=samples)
results=dba.count(results, minOverlap=1)
counts=dba.peakset(results, bRetrieve=T, DataType=DBA_DATA_FRAME)
results=dba.contrast(results, results$masks$G, results$masks$M, unique(Condition)[2], unique(Condition)[3], 
minMembers=min(c(table(Condition))), categories=DBA_CONDITION) 
results=dba.analyze(results, method=DBA_DESEQ2)
dba.plotMA(results)
dba.plotVolcano(results)

When I compare the two unhealthy ones, I encounter the following error:

> dba.plotVolcano(results)
Error in pv.DBAplotVolcano(DBA, contrast = contrast, method = method,  : 
  object 'sigSites' not found
In addition: Warning message:
No sites above threshold 
> dev.off()

Does someone know what can be wrong in this case? I couldn´t find any thread about this DiffBind problem. Thank you in advance!

Computer and R Specifications:

platform x86_64-apple-darwin15.6.0
arch x86_64
os darwin15.6.0
system x86_64, darwin15.6.0
status
major 3
minor 5.2
year 2018
month 12
day 20
svn rev 75870
language R
version.string R version 3.5.2 (2018-12-20) nickname Eggshell Igloo

DiffBind R ChIP-Seq • 945 views
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0
Entering edit mode
2.3 years ago

It seems that there simply aren't any sites that are different between your two unhealthy samples.

You can check this, e.g.:

min(results$FDR)

You can probably still get a volcano plot by changing the threshold, i.e. dba.plotVolcano(results, UsePval=1)

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