In two different cases I have received the same error when running chicagoPipeline. The first is when I provide four different .chinput files and use readAndMerge to call interactions on the combined dataset (it works fine with two files). The second is when I merge two .bam files and generate a single .chinput file from this and attempt to call interactions. The error seems to occur during the binning step of normaliseOtherEnds.
Many thanks for your help.
cd <- setExperiment(designDir = "./") files <- c("1.chinput", "2.chinput", "3.chinput", "4.chinput") cd <- readAndMerge(files=files, cd=cd) cd <- chicagoPipeline(cd) *** Running normaliseBaits... Normalising baits... Reading NPerBin file... Computing binwise means... *** Running normaliseOtherEnds... Preprocessing input... Computing trans-counts... Filtering out 365 other ends with top 0.01% number of trans-interactions Binning... Error in if (cj == upper) next : missing value where TRUE/FALSE needed In addition: Warning message: In (1:g) * nnm : NAs produced by integer overflow