DiffBind error while converting DBA object to SummarizedExperiment
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svohra • 0
@svohra-11397
Last seen 7.6 years ago
Cambridge

Hi,

I am getting the following errors while using DiffBind to output the peakset .

dba(data, bSummarizedExperiment=TRUE)
Error in FUN(X[[i]], ...) :
  assay rownames() must be NULL or equal rowData rownames() / rowRanges
  names()

Any suggestions?

 

DiffBind • 729 views
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Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK

This looks like a regression in DiffBind 2.0, , I'll check in a fix soon.

As a workaround, it does work if you use all of the peaks instead of only those in at least two peaksets:

> newData <- dba(data, bSummarizedExperiment=TRUE, minOverlap=1)

-Rory

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Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK

OK I checked in a fix that will be released in the next build as DiffBind 2.0.8.

A final note: this bug will only apply to "peaks" based DBA objects; once you start using a count-based object it worked OK.

-Rory

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