I downloaded the CGP cell line project expression data and would like to convert the affy probes to official gene symbols. It's the HG U133A v2 platform and the dataset has a total of around 22000 probes. What's the best way to do this? I tried using IDconverter, but it froze after around 100 genes. When I used DAVID to convert to official gene symbol, the results only had about 9800 genes. Using DAVID to convert to entrez returned about 24000 ids, as for some probes, multiple entrez gene ids were returned. How should I deal with these duplicated entrez ids, or is there a better way to do the conversion altogether? Thanks!
I just tried to figure it out today, The code provided by Diwan, is for Rats, it depends which type of Samples you used, Human/Rat/Mouse etc and also it depends on R and Bio conductor versions. I am using R 3.3.2 and Bioconductor 3.4. The following codes works for me, but I am not able to see all Probe IDs ( Keytype = "PROBEID") got results for only few genes.
However, Affymetrix id information is present in Thermofisher database. https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-annotation-files.html
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.
Analogous mapping questions been asked continuously (here and elsewhere) over at least a decade because no one (?) ever made a decent 3' UTR probe set that would have had much cleaner gene mappings including paralogue resolution
4 years on so this will never happen?