[BioC] chipAlongChrom problem in Ringo

Joern Toedling toedling at ebi.ac.uk
Thu Jan 22 18:38:05 CET 2009


are the warning messages any indication what the source of the problem
might be? Does the probeAnno object that you use really correspond to
the microarray platform of your ExpressionSet "X"? Maybe you
accidentally used a probeAnno from another array platform.
Are there actually any probes mapping to this region that you wanted to
plot. The region is selected by specifying the argument "xlim" as c
(<the start site that you want>, <the end site that you want>).

Try something like

table(probeAnno["5.index"] %in% featureNames(X))

to see how many probes in your probeAnno are actually defined on your array.

Try different chromosomes and regions to figure out what is wrong.
Potentially you may have to rebuild the probeAnno object for that array.


PS: Please also always provide the output of sessionInfo() when asking
questions on this list, so we can figure out if outdated or conflicting
versions of certain packages could be a source of problems.

Jianping Jin wrote:
> 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

Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk

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