[BioC] chipAlongChrom problem in Ringo

[Joern Toedling]

Jianping Jin wrote:
> table(probeAnno["5.index"] %in% featureNames(X))
>
> FALSE
> 21152

well, none of the probes seems to be included in the names of the probes
on your arrays.
How did you create the object "X"? Can you show me the output of
str(probeAnno["5.index"])
str(probeAnno["5.start"])
str(probeAnno["5.end"])
## and for comparison:
str(probeAnno["1.index"])
str(probeAnno["1.start"])

# And what is
str(featureNames(X))
featureNames(X)[1:30]
str(X)
dim(X)


>
> What are feature names in probeAnno? Actually I used a new output file
> from the script you edited to generate probeAnno with no complain:
>
> probeAnno <-
> posToProbeAnno("C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_new.txt")
>
>    Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16 17
> 18 19 2 3 4 5 6 7 8 9 X Y Done.
> allChrs <- chromosomeNames(probeAnno)
> genome(probeAnno) <- "M. musculus (mm9)"
> arrayName(probeAnno) <- "2007-02-27_MM8_CpG_Island_Pro_Tiling"

This looks alright to me. I think the function is working, but somehow
the probeAnno does not seem to match your data ExpressionSet.

Maybe can you also provide me with the first few lines of this file,
just to be sure?
C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_new.txt

Joern