Hello Roberta- Looking at where this line occurs in the code, it is in a check for the existence of the .bam file (and possibly the associated .bai file). Are the file paths correct? Is the index (.bam/bai) file there as well? If not, I can have a look at what may be happening if I can get access to some of your project data. I'm interesting in seeing your sample sheet (csv file) and the DBA object you got back form dba() before you call dba.count(). You should be able to mail these to me. Cheers- Rory On Mon Apr 14 18:41:52 CEST 2014 Roberta Sanfilippo [guest] guest at bioconductor.org wrote: > Hello! > I am using the DiffBind package to search for differences in histone modifications of ChIPseq peak data, I created a .csv files using sorted.bam > files as both bamReads and Bamcontrol and bed files as Peaks column. I tried to count reads using the dba.count function and changing the value > minOverlap from 0 to 4, but every time I obtained: > Error in if (res[i] == -1) { : missing value where TRUE/FALSE needed > WOuld you help me please? > thank you > Roberta [[alternative HTML version deleted]]