[BioC] gene.strip exonmap

Paul Hammer Paul.Hammer at p-t-p.de
Mon Mar 3 14:22:05 CET 2008

hi members,

i have some questions for the function gene.strip() from package 
exonmap. in the manual stands :

    "At its simplest, takes a list of genes and an ExpressionSet object
     and plots their data coloured by expression.  Each row of the plot
     corresponds to a gene, and the X axis corresponds to position
     within that gene. By default the plot shows only exons. Each exon
     is represented by a rectangle, coloured using the expression data
     (see below), and introns are ignored. Overlapping exons are
     plotted next to each other, and if multiple probesets hit an exon
     they are stacked vertically within the exon. Data are filtered (by
     default) to remove multiply targeted probesets. If there are no
     'well-behaved' probesets hitting an exon, it is drawn as a
     rectangle in the 'no.data.col', which is, by default, white."

but when i compare the number of the exonic probesets 
(http://xmap.picr.man.ac.uk/#21/42946926/16/h) with the number of the 
rectangles i have observed differents. for example PDE9A 
(ENSG00000160191) has according to xmap 
(http://xmap.picr.man.ac.uk/#21/42946926/16/h) 24 exonic probesets but 
the gene.strip plot (see attached file "PDE9A_Genestrip_FC breast vs 
cerebellum.png") shows 35 exons without multiple probesets. any suggestions?

R code:
 > gene.strip(c("ENSG00000160191"), affy.rma, list(1:3, 4:6), type = 
"mean-fc", main="PDE9A Fold change breast vs cerebellum")

then i tried to generate a gene.strip with the type "splicing-index". 
but i get always plots with the same color in every exon(:... (see 
sattached file "PDE9A_Genestrip_SI breast vs cerebellum.png") . anything 
wrong in my syntax?

R code:
 > gene.strip(c("ENSG00000160191"), affy.rma, list(1:3, 4:6), type = 
"splicing-index", main="PDE9A Splicing Index breast vs cerebellum")

here my sessionInfo:
 > sessionInfo()
R version 2.6.2 (2008-02-08)


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

other attached packages:
 [1] exon.pmcdf_1.1       exonmap_1.4.3        plier_1.8.0
 [4] RMySQL_0.6-0         DBI_0.2-4            RColorBrewer_1.0-2
 [7] simpleaffy_2.14.05   gcrma_2.10.0         matchprobes_1.10.0
[10] genefilter_1.16.0    survival_2.34        affy_1.16.0
[13] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.3

loaded via a namespace (and not attached):
[1] annotate_1.16.1     AnnotationDbi_1.0.6 rcompgen_0.1-17
[4] RSQLite_0.6-8

best regards
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