User: Martin Preusse

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Posts by Martin Preusse

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Comment: C: Affy: probeset to gene expression with expresso
... True ? ;) There a lot of algorithms (i.e. papers) trying to evaluate each probeset and answer this question. E.g. this one: Jetset: selecting the optimal microarray probe set to represent a gene http://www.biomedcentral.com/1471-2105/12/474 Unfortunately, as it is so often in bioinformatics, ther ...
written 6.3 years ago by Martin Preusse50
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Comment: C: Affy: probeset to gene expression with expresso
... I am trying to figure out the same. There are ENDLESS publications dealing with exactly this topic. Obviously, different probes bind to different parts of the transcript. So they might represent different transcripts of the same gene or genomic locus. Maybe a mapping to transcript instead of gene ...
written 6.3 years ago by Martin Preusse50
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Comment: C: Affy: probeset to gene expression with expresso
... Thanks! This clarifies everything ;) I misunderstood the 'summary' part of expresso. Am Dienstag, 13. August 2013 um 17:41 schrieb James W. MacDonald: > Hi Martin, > > None of the functions in the affy package know anything about the > annotation of the various probesets, so there is ...
written 6.3 years ago by Martin Preusse50
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Comment: C: Affy: probeset to gene expression with expresso
... Hi Jim, thanks, this is a very clever (and R like) way to average the expressions on the expression matrix. In my example this would work for 'exprs(eset)' when I replace the probe set ids with gene symbols. Still, it would be great to know if can be achieved with a convenience function (e.g. expr ...
written 6.3 years ago by Martin Preusse50
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Affy: probeset to gene expression with expresso
... I am trying to get the gene level expression values from an Affy micro array, i.e. merge the values for probe sets representing the same gene. I tried to use the 'expresso' function from the affy package, but I always end up with an ExpressionSet containing probe sets, not genes. What is an easy w ...
probe affy written 6.3 years ago by Martin Preusse50 • updated 6.3 years ago by James W. MacDonald51k

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Popular Question 6.3 years ago, created a question with more than 1,000 views. For Affy: probeset to gene expression with expresso

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