I am trying to teach my students the using of DESeq2, and they are repeating the instructions contained into the vignette
And they have found a very small bug. This bug does not appear when the "old" DESeq is installed into your system. But since DESeq2 is recommended, I insisted my students to not install DESeq.
This code has been extracted from the vignette itself
> library(DESeq2) > library(pasilla) > library(Biobase) > data("pasillaGenes") Warning: namespace ‘DESeq’ is not available and has been replaced by .GlobalEnv when processing object ‘pasillaGenes’ Loading required package: DESeq Error in .requirePackage(package) : unable to find required package ‘DESeq’ In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘DESeq
As you can see, in the code example, DESeq is called instead DESeq2. It is clear to me that this error is caused because I have not installed the "old" DESeq, and that a fix is got if you install it.
But.. Should we install DESeq only for this purpose ?