Introduction

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.

Code exmaple

1. Check the platform

   !Series_platform_id     "GPL15207"

   This text was presented in my data, so I known my data were produced from GPL15207.

2. install GEOquery package (Code is not fixed )

   if (!requireNamespace("BiocManager", quietly = TRUE))
   install.packages("BiocManager")
   BiocManager::install("GEOquery")

3. Transform
   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,]

References

The manual of getGEO function

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