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

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.

ADD COMMENTlink modified 23 months ago by James W. MacDonald48k • written 23 months ago by 12021560-0020
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gravatar for James W. MacDonald
23 months ago by
United States
James W. MacDonald48k 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).

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.

ADD COMMENTlink written 23 months ago by James W. MacDonald48k
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