Error while annotating with Chipseeker
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hamaor • 0
@hamaor-9799
Last seen 2.6 years ago

I followd the Diffbind pipeline for a ChipSeq data:

peaksets2 = dba(sampleSheet="SampleSheet.csv",config = data.frame(RunParallel=TRUE, AnalysisMethod=DBA_DESEQ2, bCorPlot=FALSE, bUsePval=TRUE, minQCth=10),minOverlap = 2)

peaksets2 <- dba.count(peaksets2)
peaksets2 <- dba.contrast(peaksets2, categories=DBA_FACTOR)
peaksets2 <- dba.analyze(peaksets2,bCorPlot=FALSE)

than I tried to annotate the peaks with Chipseeker:

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakAnno_inAll = annotatePeak(peaksets2.DB, TxDb=txdb, annoDb = "org.Hs.eg.db", level = "gene")

but I keep get the same error:

> peakAnno_inAll = annotatePeak(peaksets2.DB, TxDb=txdb, annoDb = "org.Hs.eg.db", level = "gene")
>> preparing features information...         2019-02-25 14:26:15 
>> identifying nearest features...       2019-02-25 14:26:15 
>> calculating distance from peak to TSS...  2019-02-25 14:26:15 
>> assigning genomic annotation...       2019-02-25 14:26:15 
Error in `[<-.data.frame`(`*tmp*`, tssIndex, "Promoter", value = TRUE) : 
  replacement has 1 row, data has 0
In addition: Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
3: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
4: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
5: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

what do I do wrong?

annotation chipseq • 630 views
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