Formatting for Annotations with HGU95AV

Question

[yrc0313]

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!

Answer 1

[russhh]

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.

[yrc0313]

Thank you so very much!