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
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.
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