Crispin Miller schrieb:
> 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@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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>>     
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