how to use custom cdf in R to convert affyID to gene symbol?

Question

[Raheleh]

I used hgu133plus2.db and annotate package in R to convert affymetrix probeset IDs to gene symbols however, I got "NA" for some IDs. I found that using "custom cdf" in stead of cdf which is provided by affymetix may solve this problem. So, I downloaded the custom cdf from BrainArray, but I don't know how to call it in R and annotate data based on custom cdf? This is the code that I already used to annotate the data:

probeset.list <- topTable(Wt_ebFit, coef=1, number=10000, lfc=2)
biocLite("hgu133plus2.db")
library(hgu133plus2.db)
library(annotate)
gene.symbols <- getSYMBOL(rownames(probeset.list), "hgu133plus2")
results <- cbind(probeset.list, gene.symbols)

I am beginner in programming and R language, I would be very appreciated if help me with that. Thanks.emphasized text

Answer 1

[Kevin Blighe]

You can use biomaRt: A: How do I convert Affymetrix ID names to gene names

Kevin