Custom cdf files and genes
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@12021560-002-12174
Last seen 4.9 years ago

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.

cdf microarray r3.2.2 • 572 views
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@james-w-macdonald-5106
Last seen 11 hours ago
United States

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.

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