I have a list of Gene IDs from human, I would like to convert it to Affymetrix IDs,
examples gene IDs
GNAI1 HLA-DQA1 WDR1 LTBP2 MXRA5 MMS19 SEC13 C6 IL16 FAM82A1 GBE1 TUBAL3 CYB5R3 ANXA1 APCS COL14A1
Do you know how I can do it in R and based on website?
I have tried the following ID convertors online but none of them worked
http://biodbnet.abcc.ncifcrf.gov/db/db2db.php
https://gemdbj.nibio.go.jp/dgdb/ConvertOperation.do
David only convert to three Affymetrix such as 3PRIME_IVT_ID, EXON_gene_ID and SNP_ID
http://david.abcc.ncifcrf.gov/conversion.jsp
I also tried Ensemble Biomart like below but did not convert anything
1- first I web to website
http://www.ensembl.org/biomart/martview/b3cd9cdf1c6bc6862d64b0e60934ef0e
2- select " Ensemble Genes 78" and "homo sapiens genes (GRCh38)"
3- then click on "filter" ------> "gene" -------> and then paste the example list of genes there
4- then "Attribute" ------> "External" ------> and select "Affy HG U133A probeset" Then click on "Results" but nothing showed up
If nothing showed up then you did something wrong. I used your example gene symbols (not IDs) at Ensembl BioMart and the conversion works fine (click "Results" after loading this URL). Perhaps you forgot to specify "HGNC symbol(s)" as the ID type in Filters?
This can also be done using R/biomaRt. Please search this site for numerous answers to similar questions.
Which organism and which array? There are annotation packages in Bioconductor for most common ones that can facilitate the conversion.
@Devon Ryan human cell lines like promyelocytic leukemia , breast adenocarcinoma. HG-U133A microarray platform