Transform microArray ID to gene symbol
Somethimes we need to transform gene ID of MicroArray data to gene symbol. For example, "AFFX-LysX-3_at", we don’t known what it means until we transform it.
- Check the platform
This text was presented in my data, so I known my data were produced from GPL15207.
- install GEOquery package (Code is not fixed )
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GEOquery")
I want to trasform rownames(mt) to gene symbol
#get annotation file GPL15207 <- getGEO("GPL15207", destdir = ".") tran_dt <- Table(GPL15207)
We need two column, ID and Gene symbol.
ID means raw ID, such like AFFX-LysX-3_at
Gene symbol was gene symbol that we need
tran_dt <- tran_dt[,c("ID","Gene Symbol")]
Tramsform (by your way)
mt <- mt[rownames(mt) %in% tran_dt$ID,]
The manual of getGEO function