Question: network analyses on genes or probesets
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gravatar for Markus Schmidberger
10.8 years ago by
Markus Schmidberger380 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 -- 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
ADD COMMENTlink modified 10.8 years ago by Marc Carlson7.2k • written 10.8 years ago by Markus Schmidberger380
Answer: network analyses on genes or probesets
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gravatar for Marc Carlson
10.8 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
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 >
ADD COMMENTlink written 10.8 years ago by Marc Carlson7.2k
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