Knowledge base

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.

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))
  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,]


The manual of getGEO function



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