User: olof.rundquist

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Posts by olof.rundquist

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Comment: C: makeContrasts from limma overides "i" as a varible
... ok I misidentified the problem. The spaces are not needed I just needed to specify that it was a contrast vector and everything worked fine. I had tried this before asking the question in the first place but I guess I must have misspelled it. makeContrast does not seem to throw and error if you do a ...
written 4 weeks ago by olof.rundquist0
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Comment: C: makeContrasts from limma overides "i" as a varible
... Thanks for the solution. So in summary I needed to added some extra spaces everywhere and then it worked like above. That's fine I guess, normal R syntax, but why do I need two spaces before the last parantheses. It does not work without it. Thanks You can close this ticket now Best Olof Rundquist ...
written 4 weeks ago by olof.rundquist0
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Comment: C: makeContrasts from limma overides "i" as a varible
... Thinking about it it is probably more informative to include the design matrix and the model function: > eRdesign Time Condition np_R2.0m.RNA 1 1 np_R6.0m.RNA 1 1 np_R7.0m.RNA 1 1 np_R1.30m.RNA 2 1 np_R2.30m ...
written 4 weeks ago by olof.rundquist0
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Comment: C: makeContrasts from limma overides "i" as a varible
... Ok maybe the for loop is unnecessary. Although it seems like makeContrast does not correctly handel my version of the vector since if I run like above I only get the last column in my contrast matrix with the first comparison as the level. This is why I decided to use the for loop in the first place ...
written 4 weeks ago by olof.rundquist0
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makeContrasts from limma overides "i" as a varible
... # makeContrasts from limma overides "i" as a varible This is not really a question. Instead this is a coding practice detail. Using makeContrasts inside a for loop is risky since it globally overwrites the variable i. This leads to unexpected behavior, see example. This is of course easily solved by ...
limma written 4 weeks ago by olof.rundquist0 • updated 4 weeks ago by James W. MacDonald51k

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