17 months ago by
The probeset IDs for the MBNI custom cdfs are the database ID concatenated to _st. So e.g., if you were using the Entrez Gene version, given an Entrez Gene ID of 1223, the probeset ID would be 1223_st.
If we assume you have run rma to get an ExpressionSet (that you called 'eset'), you can then make a featureData slot that includes all the annotation by doing something like (assuming this is human).
egids <- gsub("_st", "", featureNames(eset))
adf <- data.frame(PROBEID = featureNames(eset),
SYMBOL = mapIds(org.Hs.eg.db, egids, "SYMBOL", "ENTREZID"),
ENTREZID = egids,
GENENAME = mapIds(org.Hs.eg.db, egids, "GENENAME","ENTREZID"))
featureData(eset) <- AnnotatedDataFrame(data = adf)
Now if you process your data using limma, the annotation data will end up in the topTable output.