User: j.iremonger

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Posts by j.iremonger

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Comment: C: Limma: Best way to analyse treatment response in patients paired pre/post treatm
... Thanks again Gordon, The first contrast was what I was thinking of, but I hadn't thought of comparing them like the second. I will give that a go too.  ...
written 2.1 years ago by j.iremonger0
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Comment: C: Limma: Best way to analyse treatment response in patients paired pre/post treatm
... Hi Gordon, Going through that example has got me most of the way. I'm also interested in what unique changes are present in responders when they are given treatment. Is the below contrast valid for that comparison? makeContrasts(genes.of.interest = (Responder.treated-Responder.naive) - (Non_Respo ...
written 2.1 years ago by j.iremonger0
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Comment: C: Limma: Best way to analyse treatment response in patients paired pre/post treatm
... Thank you Gordon, you really must hate people who fail to read the entire manual!  I do apologise, it never registered with myself that this was what I was after when first reading through. ...
written 2.1 years ago by j.iremonger0
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Comment: C: problems in reading a file in AgiMicroRna package
... Hi Neela, I don't know the answer to your problem I'm afraid. The only thing I can think of is when I ran these arrays a few years back there was an issue initially with the feature extraction on the scanner. It essentially defaulted to saving a minimal reduced output rather than a `full` output. T ...
written 2.1 years ago by j.iremonger0
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Comment: C: Limma: Best way to analyse treatment response in patients paired pre/post treatm
... Thank you James, that's exactly what I needed. Looking at the matrix design it's unlike anything I've ever made before. It would explain why this problem, which I swear should be simple, has proven so tricky to get my head around. Again, thank you very much. ...
written 2.1 years ago by j.iremonger0
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Limma: Best way to analyse treatment response in patients paired pre/post treatment
... Dear All, I've searched and searched but still not confident with my LIMMA analysis here. Below is an example target file table to demonstrate the sort of samples I have (my n number is thankfully bigger than the table suggests). In the example, I have 4 patients all 4 have a disease. After complet ...
limma paired samples limma paired analysis written 2.1 years ago by j.iremonger0 • updated 2.1 years ago by Gordon Smyth39k

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