Hello,

I am working on microarray data, as I am new to it that's why I need your help. I want to ask that if I download custom cdf files from brain array then how would I be able to extract genes specific to my disease of interest i.e t2d. Which packages would I use to do this analysis? Can someone guide me about this?

Your help will be really valued.

Thank You.

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).

library(org.Hs.eg.db)
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.