Formatting for Annotations with HGU95AV
Hi! I was wondering if there was anyway to format using the HGU95AV2.db I want to convert Affymetrix ID to Gene Symbols and am using something like
mget(c("100_g_at", "1000_at", "1001_at"), hgu95av2GENENAME)
But the results are vertical as so:
$`1012_at`
[1] "K(lysine) acetyltransferase 2B"
$`1013_at`
[1] "SMAD family member 5"
I was wondering if there's anyway to format so it would be more like a table:
1012_at "K(lysine) acetyltransferase 2B"
1013_at "SMAD family member 5"
I have tried using Biomart but need to convert about 12,000 IDs and it cuts off too early. Thank you!
1 answer
You could simply do
symbols <- unlist(mget(c("100_g_at", "1000_at", "1001_at"), hgu95av2GENENAME))
or indeed,
symbols.df <- with(
list(x = unlist(
mget(c("100_g_at", "1000_at", "1001_at"), hgu95av2GENENAME)
)),
data.frameaffy.id = names(x), genename = x)
)
However, I'd urge you to use hgu95av2SYMBOL rather than ..GENENAME, since you state that you want to convert Affy ids to gene symbols.
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