Question

Different annotation obtained from hgu133a2.db and affymetrix annotation release

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2323982403 ▴ 60

@2323982403-11356

Last seen 3.6 years ago

Ann Arbor

I've got a lncRNA NEAT1, and I want to see its expression in one dataset from hgu133a2 platform. I found the affymetrix id '214657_s_at' was mapped to NEAT1 in affymetrix annotation release 'HG-U133A_2 Annotations, CSV format, Release 36 (19 MB, 4/13/16)'. But when I query the probeset using the following code

getEG('214657_s_at', 'hgu133a2.db')

I got an NA return. I'm wondering the difference between hgu133a2.db and the annotation release from affymetrix. Should I continue to use affymetrix annotation instead of hgu133a2.db?

annotation hgu133plus2.db affymetrix microarrays micorarray • 1.5k views

ADD COMMENT • link updated 6.0 years ago by James W. MacDonald 67k • written 6.0 years ago by 2323982403 ▴ 60

score 3 · Accepted Answer · 2018-12-01

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 5 hours ago

United States

You shouldn't be using getEG these days. The current paradigm is to use select:

> select(hgu133a.db, '214657_s_at', c("SYMBOL","ENTREZID"))
'select()' returned 1:many mapping between keys and columns
      PROBEID SYMBOL ENTREZID
1 214657_s_at  NEAT1   283131
2 214657_s_at MIR612   693197

ADD COMMENT • link 6.0 years ago James W. MacDonald 67k

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Thanks, but I'm wondering why getEG doesn't work any more.

ADD REPLY • link 6.0 years ago 2323982403 ▴ 60

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Some functions just get outdated and replaced by better and more "universal" ones. Its really tough sometimes to keep up with all the changes happening, especially towards the end of the year! Select is awesome though

ADD REPLY • link 6.0 years ago sherajilir • 0

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getEG does work. It gave you an answer without an error, no? It just gives you a different answer than what you get using select, because in the intervening period (getEG is a function that was from circa 2004 or so) we changed our mind about what you should get when a given probe measures more than one thing. In the past we returned NA because it wasn't clear what was being measured. In recent times we have decided to return all available mappings and let the end user sort it out.

You can't get multi-mapping probes using getEG, because it's a convenience function. You can use get however.

> get('214657_s_at', hgu133aENTREZID)
[1] NA
> z <- toggleProbes(hgu133aENTREZID, "all")
> get('214657_s_at', z)
[1] "283131" "693197"

ADD REPLY • link 6.0 years ago James W. MacDonald 67k