Diffbind dba.plotProfile attempt to select less than one element in OneIndex
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Entering edit mode
bhanratt • 0
@bhanratt-15265
Last seen 3 days ago
United States

Not sure what's going on with this function. I assume it's a bug. dba.analyze() ran fine without errors but dba.plotProfile() threw this:


> DBA <- dba.analyze(samplesheet, bBlacklist=FALSE, bGreylist=FALSE)
Loading sample sheet...
58 1 H3K4me3 AD  1 macs
77 2 H3K4me3 AD  2 macs
78 3 H3K4me3 AD  3 macs
81 4 H3K4me3 AD  4 macs
92 5 H3K4me3 AD  5 macs
145.1 6 H3K4me3 NE  1 macs
145.2 7 H3K4me3 NE  2 macs
173.1 8 H3K4me3 NE  3 macs
49 9 H3K4me3 NE  4 macs
93 10 H3K4me3 NE  5 macs
Forming consensus peakset and counting reads...
Computing summits...
Re-centering peaks...
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Normalize DESeq2 with defaults...
Forming default model design and contrast(s)...
Computing results names...
Analyzing...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>
> DBA.profile <- dba.plotProfile(DBA, labels=DBA_ID)
Generating report-based DBA object...
Generating profiles...
Error in value[[3L]](cond) :
  profileplyr error: Error: stop worker failed:
  attempt to select less than one element in OneIndex
DiffBind • 123 views
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Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 2 hours ago
CRUK, Cambridge, UK

I can't tell exactly what is going on from this description. It would be a good idea to check the result of the analysis prior to plotting by checking what happens when you print DBA. Another idea is to generate the report object used by dba.plotProfile() explicitly, and seeing what that looks like before passing it in.

Try running the following code and let me know what happens:

DBA <- dba.analyze(samplesheet, bBlacklist=FALSE, bGreylist=FALSE)
DBA
DBA.report <- dba.report(DBA, bDB=TRUE, bGain=TRUE, bLoss=TRUE, bAll=FALSE)
DBA.report
DBA$config$RunParallel <- FALSE
DBA.profile <- dba.plotProfile(DBA, labels=DBA_ID, sites=DBA.report)
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