Entering edit mode
hamaor
•
0
@hamaor-9799
Last seen 5.8 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?