Hi,

Could you post your sessionInfo(), so I can see what version of R and DiffBind you're running?  Also your sample sheet and the first few lines of one of your peak files?  Or email them to me, if you'd rather not post them publicly (email available on DiffBind's Bioconductor page).  Also the output of "traceback()" immediately after the error might help. - Gord

Hi Gord,

Thanks for your answer. The dba.count problem is solved partially. Afterwards, it seems not all of the samples get the '"FRiP"score, and I could not plot it. Then I thought the computer may not have enough memory. So I tried on a PC with bigger memory. But still does not work, Could you please have a look and help me out from here.

> SCFIL = dba.count(SCFIL, minOverlap = 1)
Error: Error processing one or more read files. Check warnings().
In addition: Warning messages:
1:  
2:  
3:  
4:  
5:  
6:  
7:  
> traceback()
3: stop("Error processing one or more read files. Check warnings().",
       call. = FALSE)
2: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,
       bLog = bLog, insertLength = insertLength, bOnlyCounts = T,
       bCalledMasks = bCalledMasks, minMaxval = filter, bParallel = bParallel,
       bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl,
       filterFun = filterFun, bLowMem = bUseSummarizeOverlaps, readFormat = readFormat)
1: dba.count(SCFIL, minOverlap = 1)

First Output (PC with small memory)

> SCFIL = dba.count(SCFIL, minOverlap = 1)
> SCFIL
6 Samples, 18962 sites in matrix:
               ID   Tissue  Factor   Condition Replicate Caller Intervals FRiP
1   Stemcell_K4_I stemcell H3K4me3 stemcell_K4         1 counts     18962 0.70
2  Stemcell_K4_II stemcell H3K4me3 stemcell_K4         2 counts     18962 0.65
3 Stemcell_K4_III stemcell H3K4me3 stemcell_K4         3 counts     18962 0.65
4        FIL_K4_I      FIL H3K4me3      FIL_K4         1 counts     18962 0.76
5       FIL_K4_II      FIL H3K4me3      FIL_K4         2 counts     18962     
6      FIL_K4_III      FIL H3K4me3      FIL_K4         3 counts     18962     
> plot(SCFIL)
Fehler in if (sd(v2) == 0) { : Fehlender Wert, wo TRUE/FALSE nötig ist

> traceback()
6: pv.pairs(pv, mask = mask, CorMethod = CorMethod, bPlot = bPlot,
       minVal = minVal, bCorOnly = bCorOnly, bNonZeroCors = bNonZeroCors)
5: pv.occupancy(DBA, mask = mask, sites = sites, Sort = "cor", bCorOnly = T,
       CorMethod = distMethod)
4: dba.plotHeatmap(x, ...)
3: plot.DBA(SCFIL)
2: plot(SCFIL)
1: plot(SCFIL)

Thanks