Dear list, Although not directly related to BioC, I would appreciate any pointer to papers/methodology related to the question of how to calculate a pathway score (for e.g. pathways defined by KEGG) for an individual array. TIA, Guido Background: we standardly use methodology like GSEA to find pathways that are regulated upon treatment compared to control. For example, GSEA calculates a 'pathway score' (the Normalzed Enrichment Score NES) by combining and comparing expression data from all replicates from an experimental and control groups. We now would like to calculate a pathway score for each individual array (thus like having an expression estimate per array for a probeset, but now for a pathway), but i don't know how to approach this. ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]

Hello Guido: I am just curious how combining gene expression measurement into a gene-set measurement ("pathway score") would affect the downstream statistical tests, if any, to be later performed on these scores. For example, in case of simple GSEA [1]: (a) per-gene t-statistics have a t-distribution, and (b) assuming observed t-statistics are independent. Combined these two lead to: sum of t-statistics taken over genes in a gene set divided by the square root of number of genes should have approximately normal distribution. This property can then be used to find outliers (interesting pathways). I wonder if there is anything similar for gene expression measurements? Best wishes, Saroj [1] Section 13.1.1. of Chapter 13 of Bioconductor case studies by Hahne et al (Springer) pp.194-195 Hooiveld, Guido wrote: > Dear list, > > Although not directly related to BioC, I would appreciate any pointer to > papers/methodology related to the question of how to calculate a pathway > score (for e.g. pathways defined by KEGG) for an individual array. > > TIA, > Guido > > Background: we standardly use methodology like GSEA to find pathways > that are regulated upon treatment compared to control. For example, GSEA > calculates a 'pathway score' (the Normalzed Enrichment Score NES) by > combining and comparing expression data from all replicates from an > experimental and control groups. We now would like to calculate a > pathway score for each individual array (thus like having an expression > estimate per array for a probeset, but now for a pathway), but i don't > know how to approach this. > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >