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Genekitr: An R Toolkit for Gene Analysis

6 Probe ID conversion

Probes are used to measure the expression level of many genes. After getting microarray data, the first important step before downstream analysis is probably probe ID conversion.

Ensembl database regularly maps probe sets against the latest set of transcript models using their own pipeline.

Here, transProbe utilizes Ensembl’s up-to-date annotation datasets and can be seamlessly combined with other genekitr functions.

Notice: now we only support human data

6.1 Supported platforms

There are 36 supported probe platforms, including Affymetrix, Agilent, Illumina, Codelink and Phalanx.

DT::datatable(hsapiens_probe_platform, options = list(pageLength = 10))

6.2 Basic usage

transProbe has four arguments:

  • id: probe ID
  • transTo: the conversion target type. Users can select more than one from “symbol”, “entrez”, “ensembl” or “uniprot”.
  • org: human (default)
  • platform: Probe platform. If not given, the program will detect it automatically.
data(deg, package = "genekitr")
probes <- deg$probe_id

res <- transProbe(probes, transTo = "ensembl", org = "human")
head(probes)
## [1] "8144866" "8066431" "8022674" "7925531" "8081358" "7979931"
head(res)
## # A tibble: 6 Ă— 2
## # Groups:   probe_id [6]
##   probe_id ensembl        
##   <chr>    <chr>          
## 1 8144866  ENSG00000156006
## 2 8066431  ENSG00000196839
## 3 8022674  ENSG00000170558
## 4 7925531  ENSG00000275199
## 5 8081358  ENSG00000256628
## 6 7979931  ENSG00000133997

6.3 Convert to more than one type

Users can define transTo with multiple types:

res2 <- transProbe(probes, transTo = c("ensembl","symbol"), org = "human")
head(res2)
##       probe_id         ensembl     symbol
## 9023   8144866 ENSG00000156006       NAT2
## 15007  8066431 ENSG00000196839        ADA
## 11595  8022674 ENSG00000170558       CDH2
## 17512  7925531 ENSG00000275199       AKT3
## 17126  8081358 ENSG00000256628 ZBTB11-AS1
## 6218   7979931 ENSG00000133997       MED6

Let’s take the first record as an example: ENSG00000228794 has 38 transcripts.

When we look at its second transcript ENST00000445118.7, probe 7896759 is listed in the AFFY HuGene-1_0-st-v1 database.