Sorry if this is obvious, but I was wondering how do people use custom cdf with oligo package ?
I downloaded the cdf version 20 from column 'O' for the hugene20 st array (pd.hugene20st.hs.entrezg_20.0.0.tar.gz) and installed the package and I tried to do something like this:
dat <- read.celfiles(filenames = list.celfiles(), pkgname = "pd.hugene20st.hs.entrezg")
and when I do:
The class of dat is GenericFeatureSet instead of GeneFeatureSet which can not be use by rma pre-processing later on. Do people convert the GenericFeatureSet to GeneFeatureSet? or am I missing any steps when using the cdf file?