Hello,

I have microarray data from the chip [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], and I am trying to annotate the probe IDs in R using the hugene10sttranscriptcluster.db package and the following function:

    annotatedTopTable <- function(topTab, anotPackage)
    {
      topTab <- cbind(PROBEID=rownames(topTab), topTab) 
      myProbes <- rownames(topTab)
      
      thePackage <- eval(parse(text = anotPackage)) 
      
      geneAnots <- AnnotationDbi::select(thePackage, myProbes, c("SYMBOL", "ENTREZID", "GENENAME")) 
      
      annotatedTopTab<- merge(x=geneAnots, y=topTab, by.x="PROBEID", by.y="PROBEID") 
    return(annotatedTopTab)
    }

    topAnnotated_Condition<- annotatedTopTable(topTab_Condition,
    anotPackage="hugene10sttranscriptcluster.db")

    topAnnotated_Condition

 Is hugene10sttranscriptcluster.db the right package to use? 

Thanks


Yes, for most use-cases, that package is correct. It will depend on how the original array data was processed.

You only need to do this, by the way:

    require(hugene10sttranscriptcluster.db)
    mapIds(
      hugene10sttranscriptcluster.db,
      keys = probes,
      column = 'SYMBOL',
      keytype = 'PROBEID')
    
    select(
      hugene10sttranscriptcluster.db,
      keys = probes,
      column = c('SYMBOL', 'ENTREZID', 'ENSEMBL'),
      keytype = 'PROBEID')

Kevin
