Hi Everyone,
I recently had to reformat my mac to get the OSX Yosemite. Now I run into the problem that the oligo package does not work.
The reason seems to be that for the .CEL files that I am using (at the read.celfiles step) the oligo package requires the annotation package pd.ht.mg.430.pm, which is not in the repository (anymore?): https://www.bioconductor.org/packages/release/data/annotation/
Has anybody run into this problem? The 430 PM it is a very common affymetrix platform that did not cause any problems in the oligo package before (I am using unchanged R script that was previously working).
http://www.affymetrix.com/catalog/131444/AFFY/HT+MG-430+PM+Array+Plate#1_3
Any comments/suggestions are welcomed. I am on the brink of trying figuring out how to build my own annotation package from here:http://www.bioconductor.org/packages/release/bioc/vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf
Thanks!
Peer
There is a package called pd.ht.mg.430a; is that the one you are looking for?
http://www.bioconductor.org/packages/release/data/annotation/html/pd.ht.mg.430a.html
Thanks for the reply, but no unfortunately that is not it. It may be similar enough with the same annotation but the oligo package specifically asks for "pd.ht.mg.430.pm", while it loads the "pd.ht.mg.430a" annotation just fine.
Here's the full error code:
> affyRaw <- read.celfiles(celFiles)
Loading required package: pd.ht.mg.430.pm
Attempting to obtain 'pd.ht.mg.430.pm' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.ht.mg.430.pm' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in read.celfiles(celFiles) :
The annotation package, pd.ht.mg.430.pm, could not be loaded.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.ht.mg.430.pm’
It says that pdInfoBuilder can help you. Perhaps you can use pdInfoBuilder to create the package you need. I don't know much about it but perhaps someone else can chime in.
http://bioconductor.org/packages/release/bioc/html/pdInfoBuilder.html
Thanks! That was going to be my last resort. I linked the pdInfoBuilder at the end of the original post, too.