[BioC] gene.strip exonmap

[Crispin Miller]

Hi Paul,
Sometimes transcripts have exons with different lengths that overlap each
other in the gene. Gene strip will draw a separate rectangle for each of
these, orderered, I think by the start location of each of the exons.
Genestrip was written originally to let you summarise lots of genes in a
single figure, so it's a tradeoff between complexity in the plot and showing
less information. 

In situations like this, if you use 'plot.gene', or 'gene.graph' you should
be able to see more detail that can help you distinguish between the
different cases...

Crispin



On 3/3/08 13:22, "Paul Hammer" <Paul.Hammer at p-t-p.de> wrote:

> 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)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L
> C_MONETARY=en_US.UTF-8;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] 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
> paul
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