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 -------------- next part -------------- A non-text attachment was scrubbed... Name: PDE9A_Genestrip_FC breast vs cerebellum.png Type: image/png Size: 7777 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20080303 /efc20ce4/attachment.png -------------- next part -------------- A non-text attachment was scrubbed... Name: PDE9A_Genestrip_SI breast vs cerebellum.png Type: image/png Size: 7350 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20080303 /efc20ce4/attachment-0001.png

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_IDENTIFICA TION=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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}