Hi,

when I run the example in the makeBackground help file with the quick option set to "F", I get an error:

Error in motifScores(bg, pwms, verbose = verbose) : 
  Sequence with index(es): 49007,49008,49171,49172,49173,49174 only contain N's. Please remove this sequence as the PWM score cannot be computed for any position.

I get the same error when I try it with my custom PWMs.

How should I generate the background for my PWMs properly?

Thanks,

Deniz

Here the code from the help file:

# load in the two example de-novo motifs
motifs = readMotifs(system.file(package="PWMEnrich", dir="extdata", file="example.transfac"), remove.acc=TRUE)

## Not run: 
# construct lognormal background
bg.logn = makeBackground(motifs, organism="dm3", type="logn")