Question: Custom cdf files and genes
gravatar for 12021560-002
17 months ago by
12021560-0020 wrote:


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.

ADD COMMENTlink modified 17 months ago by James W. MacDonald46k • written 17 months ago by 12021560-0020
gravatar for James W. MacDonald
17 months ago by
United States
James W. MacDonald46k wrote:

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(, egids, "SYMBOL", "ENTREZID"),
                         ENTREZID = egids,
                         GENENAME = mapIds(, 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.

ADD COMMENTlink written 17 months ago by James W. MacDonald46k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 142 users visited in the last hour