My guess is that your sample sheet is tab-separated, not comma-separated.
The output message surprising as it prints out not only the
PeakCaller, but also the paths for
Peaks. There isn't anyplace in
DiffBind where that happens! (I just did some greps of the source code to confirm that).
Something is causing
DiffBind to pick up the values for multiple columns as a single value. As a result, by the time it looks to read the
PeakCaller, there is nothing there so it defaults to
raw. The error you are seeing is consistent with this, as
raw looks in the fourth column for the score; in MACS2 broad peaks format, the fourth column is a name string which can not be coerced into a numerical value to treat as a score, which cases that error. (Note to self: I should catch this condition and print out a more informative error message.)
Have a close look at the sample sheet. This should be a
.csv file, which means it should be comma-separated, not tab separated. Check to see if there really is exactly one comma between each column. If it is a well-formed
.csv file, you can send it to me (
IRF5_Samples_Descr.csv) and I'll have a look at what is going on internally.