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Paul Hammer
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220
@paul-hammer-2635
Last seen 10.3 years ago
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;LC_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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