[BioC] ChIPpeakAnno, callEnrichedRegions results have "holes"

[Susan Wilson]

Hi,

I have some ChIP-seq data which returns a fairly uniform set of scores 
with the computeMATScore function. When I export (rtracklayer) that data 
as a .wig file, IGV visually reinforces that fact. However, when I run 
callEnrichedRegions, no matter how I try and "relax" the thresholds, 
using either method = score, pValue, or FDR, the resulting (bedgraph) 
data has single contiguous "holes" in regions of yeast chromosomes IV, 
X, XII, XIII, XV, and XVI (note, the chromosomes are not completely 
blank). The wiggle plot shows no obvious qualitative differences in 
those regions. Has anyone seen this behavior?

Thanks.
Susan