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willkjh avatar willkjh commented on July 30, 2024

In the older .Rpres file, biocLite is already installed or placed in the code. Refer to https://github.com/raphg/Biostat-578/blob/master/Differential_expression.Rpres
You should take a look at the course outline and follow the series of lectures. https://github.com/raphg/Biostat-578

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brianhigh avatar brianhigh commented on July 30, 2024

None of the Rpres files for this currently install limma or edgeR.

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willkjh avatar willkjh commented on July 30, 2024

Look at line 293 -295 of https://github.com/raphg/Biostat-578/blob/master/Differential_expression.Rpres

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brianhigh avatar brianhigh commented on July 30, 2024

Okay for limma. But what about edgeR? And why not make each presentation run independently of the others? Perhaps using require would be a good compromise, so as to avoid reinstalling packages in each file if they are already present? The point here is to minimize the amount of "gotchas" for a student, especially those new to R. Good programmers make their code as user-friendly as they can, especially when the language already provides tools like require to make it easy.

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raphg avatar raphg commented on July 30, 2024

In general, I think it's ok to expect users to install the packages. require does not actually help, see http://stackoverflow.com/questions/5595512/what-is-the-difference-between-require-and-library

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