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


ADD COMMENTlink written 6 months ago by Kevin Blighe52k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1407 users visited in the last hour