Question: how to use custom cdf in R to convert affyID to gene symbol?
1
gravatar for Raheleh
3.1 years ago by
Raheleh120
Raheleh120 wrote:

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

ADD COMMENTlink modified 6 months ago by Kevin Blighe52k • written 3.1 years ago by Raheleh120
0
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe52k
Kevin Blighe52k wrote:

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

Kevin

ADD COMMENTlink written 6 months ago by Kevin Blighe52k
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