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 data("pasillaGenes") Warning: namespace ‘DESeq’ is not available and has been replaced by .GlobalEnv when processing object ‘pasillaGenes’ Loading required package: DESeq Error in .requirePackage(package) : unable to find required package ‘DESeq’ In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 ?
Can you post your sessionInfo() please?
The vignette uses the pasilla data package which requires DESeq (original package). When you install pasilla using biocLite(), everything you need should be installed.
How did you install pasilla?