I am following the gcMap vignette:
The following data takes a long time to load so I have commented it out:
library( ArrayExpress ) library( affy ) # GEOD5258.batch <- ArrayExpress("E-GEOD-5258")
I obtain the following error:
Loading required package: pd.u133aaofav2
Attempting to obtain 'pd.u133aaofav2' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.u133aaofav2' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in oligo::read.celfiles(filenames = file.path(path, unique(files))) :
The annotation package, pd.u133aaofav2, could not be loaded.
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.hg.u133a’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.u133aaofav2’
Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, :
Unable to read cel files in/var/folders/3j/tzl04yg97_n60yhhhr29vr_4f7byc0/T//RtmpJRYSQc
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) :
ArrayExpress: Unable to read assay data
I then tried to install the library but received the message:
pd.u133aaofav2 is not available for R3.3.2.
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):
Does anyone have any suggestions on how to resolve this? Thanks.