User: Tom Wenseleers

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Posts by Tom Wenseleers

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Comment: C: Statistical power of limma vs mixed model approach to analyze microarray and dif
... Dear Peter, So if I get your question right you want to know whether there is a difference in the log ratio estimated from the RNAseq and the proteomics data, right? The problem I think that in this case the error structure for the data sets will be completely different. Perhaps you could do an arcs ...
written 4.4 years ago by Tom Wenseleers60
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Comment: C: Statistical power of limma vs mixed model approach to analyze microarray and dif
... Dear Gordon, Many thanks for your further comments! I was aware of the model formula specification in limma, which is indeed very handy - but in my experiments I often have multiple random factors, that's the problem... And sorry meant modelMatrix of course, was looking at some old documentation for ...
written 4.4 years ago by Tom Wenseleers60
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Answer: A: Statistical power of limma vs mixed model approach to analyze microarray and dif
... Dear Gordon, Many thanks for your message! Of course, I agree with you that mixed model theory as such is pretty complicated and still to some extent in development. But what I find easier is the specification part of the model, where all you have to do is specify the formula that captures the depen ...
written 4.4 years ago by Tom Wenseleers60
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Statistical power of limma vs mixed model approach to analyze microarray and differential proteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data
... Dear all, I was just analyzing some data from a differential (dual label LC/MS) single factor peptidomics experiment using both a per-feature mixed model approach (using lme4's lmer function, using a model of the form intensity/abundance ~ (1|run)+label+treatment, and testing significance and calcul ...
rnaseq microarray go limma edger deseq written 4.4 years ago by Tom Wenseleers60 • updated 23 months ago by Gordon Smyth32k
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Averaging duplicate probes in an RGList object
... Dear all, On my microarray I have some genes for which I have duplicate probes, but not for all. Before I do the stats I would like to average the duplicate probes (e.g. GB10001-RA and GB10006-RA in the example below). So I have a limma RGList object, with the gene names stored in RG$genes$GeneName ...
microarray probe limma written 7.7 years ago by Tom Wenseleers60
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Using Limma for proteomics (2D DIGE) datasets
... Dear all, I am interested in using Limma/LimmaGUI for the analysis of proteomics (2D DIGE) datasets. I have had a try with LimmaGUI, however, I seem to keep on getting the message "limmaGUI was unable to read in the gene list from the raw (image analysis) files." (although the Cy3 and Cy5 data are r ...
proteomics limma impute limmagui written 8.1 years ago by Tom Wenseleers60 • updated 2.4 years ago by sm0

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