network analyses on genes or probesets
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@markus-schmidberger-2240
Last seen 9.6 years ago
Hi all, I am using affymetrix microarray data. In the raw data I have probes. After preprocessing (background correction, normalization and summarization) I have probesets. Now I can use the annotation packages (e.g. library(hgu133a.db)) to get the assignment between probesets and genes. Are there any functions, methods (median, mean,...), literature how to combine probesets to genes? I want to run some network analyses on gene level. Therefore I need some kind of 'gene intensity'. Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4497
Microarray Annotation Normalization Preprocessing Network Microarray Annotation Network • 858 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
United States
Hi Markus, One thing you could if you want to go from many probesets to single genes, is to use the nsFilter() from the genefilter package to retain the "high variance" probesets. This will not "combine" probesets, but instead can be used to jettison all but one probeset (for each gene) that seems likely to maybe be measuring something. It also has a parameter that will let you only get back things that actually have an entrez gene ID. Here is a link in case this sounds like something you might want to pursue this strategy: http://www.bioconductor.org/packages/release/bioc/html/genefilter.html Marc Markus Schmidberger wrote: > Hi all, > > I am using affymetrix microarray data. In the raw data I have probes. > After preprocessing (background correction, normalization and > summarization) I have probesets. Now I can use the annotation packages > (e.g. library(hgu133a.db)) to get the assignment between probesets and > genes. > > Are there any functions, methods (median, mean,...), literature how to > combine probesets to genes? > > I want to run some network analyses on gene level. Therefore I need > some kind of 'gene intensity'. > > Thanks > Markus >
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