Thanks for advising me to post the question to the main Bioconductor forum.
When trying to read in the peaksets with a command like this:
I get this error message:
Error in Summary.factor(c(59L, 15L, 56L, 12L, 21L, 23L, 43L, 52L, 28L, :
‘max’ not meaningful for factors
I don’t have a PeakFormat column in the filename .csv file, and I am using BED files generated by Homer2. The BED files are plain tab delimited txt files with 4 columns; the 4th column has the peak scores in a format chr#-value.
I found that the deletion of the 4th column solves the problem and the peaksets are read in.
The question is if the peak scores are considered by DiffBind at all, and if the problem that arises later on (no way to get beyond factorname = dba.analyze(factorname) is a result of the reading in the peaksets?
Thanks in advance,