[BioC] chipAlongChrom problem in Ringo

[Jianping Jin]

Hi list,

I ran into a problem using chipAlongChrom to visualize a Chip chip array 
intensities:

> chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2, 
xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S
et2")
Getting probe intensities in selected regions..,
Preparing color scheme...
Plotting intensities...
Obtain genomic features...
Warning messages:
1: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff = 
mm9genes2,  :
  The identifiers of 28 reporters in the region to plot are not found as 
'featureNames' of X

2: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff = 
mm9genes2,  :
  Only NA values in specified region.

A plot came up and could display everything except intensity data which are 
supposed to center around the dashed zero line. This function uses gff, 
probeAnno and expression set files. What file(s) should I check, or a 
script issue?

Thanks,

Jianping

##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu