[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi

Question

[appropiate]

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

Answer 1

[Kevin Blighe]

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

[appropiate]

Thanks! I actually had the function because I also wanted to have the table with values related to differential gene expression (logFC, pval,...) in the final annotated table, and because I had several tables to annotate.