I want to annotate probe IDs from Affymetrix GeneTitan U219 Array in R.
For that purpose I use Bioconductor package hgu219.db, to retrieve just EntrezGene IDs.
However, there are quite a lot of probe IDs that do not seem to be present in hgu219.db, up to 3000+ in my list of 49000+
This is a MWE:
#source("https://bioconductor.org/biocLite.R") #biocLite("hgu219.db") library(hgu219.db) xx.df <- as.data.frame(hgu219ENTREZID) subset(xx.df, probe_id %in% c("11715106_x_at","11715107_s_at","11715111_s_at","11715138_s_at","11715140_s_at"))
I just included 5 of the probes I cannot annotate, which seem pretty standard; in fact, I can find them in the table here, and they all seem to have EntrezGene ID annotation.
So my question is: Is there a reason why these probes are not listed in hgu219.db? Is there any other preferred way to annotate them in R?