[BioC] chipAlongChrom problem in Ringo

[Jianping Jin]

Thanks for your quick reply.

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

FALSE
21152

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"

FYI
> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] biomaRt_1.16.0      topGO_1.10.1        GO.db_2.2.5
 [4] RSQLite_0.7-1       DBI_0.2-4           graph_1.20.0
 [7] ccTutorial_1.0.0    Ringo_1.6.0         SparseM_0.78
[10] RColorBrewer_1.0-2  vsn_3.8.0           affy_1.20.2
[13] limma_2.16.4        geneplotter_1.20.0  annotate_1.20.1
[16] xtable_1.5-4        AnnotationDbi_1.4.2 lattice_0.17-17
[19] genefilter_1.22.0   survival_2.34-1     Biobase_2.2.1

loaded via a namespace (and not attached):
[1] affyio_1.10.1        cluster_1.11.11      grid_2.8.1
[4] KernSmooth_2.22-22   preprocessCore_1.4.0 RCurl_0.94-0
[7] XML_1.99-0

Jianping

--On Thursday, January 22, 2009 5:38 PM +0000 Joern Toedling 
<toedling at ebi.ac.uk> wrote:

> Hello,
>
> 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.
>
> Regards,
> Joern
>
> 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
>



##################################
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