I attempted the run DiffBind (v3.4.0) for my samples ( I have bam, control bam and peak files in the sample sheet). After running about 5 hrs, it returns the following error. Any idea what causing this?
dba_obj <- dba(sampleSheet=Sample) dba_obj <- dba.count(dba_obj, bUseSummarizeOverlaps=TRUE) 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. ... Error in SummarizedExperiment(assays = SimpleList(counts = countData), : the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object (or derivative) to construct Calls: sourceWithProgress ... withCallingHandlers -> <Anonymous> -> SummarizedExperiment In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted
dba.count , it seems to work but that means I have to use all the peak set for the analysis
dba_obj <- dba.count(dba_obj, minOverlap=1 )