given the several requests I got re: supporting HTA 2.0 chips when using
oligo, I'm posting this message to bioc (rather than bioc-devel).
I'll add support for HTA on our next release. A draft is ready through the
devel branch. I may need to make some adjustments prior to the April
For those interested in giving it a try, you'll need to have a developer
installation of Bioconductor (please, make sure to use a different path to
set your library and avoid mixing & matching). Then install oligo v.
1.27.3. With the devel bioc installed, you can use the usual:
You will also need an annotation package specific for HTA, which you can
download from here: (source version only)
After downloading the annotation package, install it using:
## assuming that you loaded R from the directory where the
## package was downloaded to.
Once both are installed, you should be able to run the standard:
cels = list.celfiles()
raw = read.celfiles(cels)
pp0 = rma(raw, target='core')
pp1 = rma(raw, target='probeset')
to obtain your preprocessed data through oligo.
The annotation package will be made available through Bioconductor in the
next few weeks (devel branch again).
If you're in the mood of building your own annotation package, after
ensuring you have the aformentioned packages (and versions) installed, also
install pdInfoBuilder (version 1.27.4). Then, you can use the template
below to create your package:
## code to build HTA annot pkg
seed <- new("AffyHTAPDInfoPkgSeed",
If you have any feedback/comment, please contact me.