User: wim.trypsteen

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Posts by wim.trypsteen

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Answer: A: limma backgroud signal
... Dear Gordon Thanks for your answer and time. I understand the exact choice of multiplier is a little bit arbitrary but I am just looking for a good way of describing the amount of expressed probes/genes in my system and 44000 expressed probes seemed a lot to me. Would the following be a good rough ...
written 4.7 years ago by wim.trypsteen0
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Answer: A: limma paired design matrix 3 factors
... Hi James Thanks again for your reply, here is a little bit more information on the experimental setup: For the experimental setup we started from 1 flask op cells and divided the cells into 2 fractions. 1 fraction we infected with wild type virus and the other fraction with a 'mock' virus (so same ...
written 4.7 years ago by wim.trypsteen0
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limma backgroud signal
... Hi all I was wondering what a good cutoff is for a truely expressed probe in the limma data analysis (single channel agilent): #filter out expressed probes from background signal: control type probes neg95 <- apply(G.norm.quant$E[G.norm.quant$genes$ControlType==-1,, drop=FALSE],2,function(x) qu ...
limma background signal written 4.7 years ago by wim.trypsteen0
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Answer: A: limma paired design matrix 3 factors
... Dear James Thanks for your answer and time. I also tried similar design matrices and that worked fine but I am specifically struggling with the pairing of the uninf to infected per experiment. (So first within experiment and than together..) I tried blocking with duplicateCorrelation but I got the ...
written 4.7 years ago by wim.trypsteen0
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limma paired design matrix 3 factors
... Hi all I've been unsuccesfully browsing forums, limma user guide to find an answer to the following question, I know there are many posts on this allready, so forgive me mine: We performed following experiment: we infected a celline with a virus and extracted RNA at 4 timepoints after infection. T ...
limma paired design and contrast matrix written 4.7 years ago by wim.trypsteen0

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