Comments (5)
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
from biostat-578.
None of the Rpres files for this currently install limma
or edgeR
.
from biostat-578.
Look at line 293 -295 of https://github.com/raphg/Biostat-578/blob/master/Differential_expression.Rpres
from biostat-578.
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.
from biostat-578.
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
from biostat-578.
Related Issues (15)
- Sequence_analysis.Rpres: need to load packages before using them
- Installing packages before loading them in *.Rpres HOT 1
- Sequence_analysis.Rpres: could not find function "melt"
- Bioconductor_intro.Rpres: Data/GEO folder does not exist
- Bioconductor_intro.Pres: use Sys.getenv("TAR") instead of "gtar" HOT 1
- RNA-seq.Rpres: replacement for T14 file HOT 5
- dbWriteTable() needs overwrite=TRUE HOT 3
- installallpkgs.R introductory comments edit
- R code to fix RNA-seq "problematic" GSE45735 file
- limma package updated: symbols2indices() renamed to ids2indices()
- typo "Rle" in Sequence_analysis.Rpres HOT 2
- Inconsistent capitalization in "images" folder name
- Sequence_analysis.Rpres: data frame versus data table problem HOT 1
- Inconsistent loading of knitr before opts_chunk setting HOT 1
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from biostat-578.