[BioC] limma topTable with gene symbols in output: annotate problem

[Carlson, Marc R]

Hi Stephen,

Can I please have the output from sessionInfo()?  It is necessary so that I know what version of R you are using etc.  For my answers below I will have to assume that you are using the latest one, but if you aren't, then all bets are off.  And have you seen the posting guide?  If not you can find it here: 

http://www.bioconductor.org/help/mailing-list/posting-guide/


Now if I test "hugene10stprobeset.db", I can see that it works for me:

ids = c("8039755","7960952","8058922","8010074","8002354")
library("annotate")
library("hugene10stprobeset.db")
getSYMBOL(ids, "hugene10stprobeset.db")

So *if* you have legitimate probe IDs, then getSYMBOL() should work for you.  But if your probe IDs are not what you think they are, then you will get all NAs...  Looking at our list of ".db packages", are you sure that you are supposed to be using "hugene10stprobeset.db" and not "hugene10sttranscriptcluster.db"?  

Also, calling getSYMBOL() on "hugene10stv1cdf" will never work, as the getSYMBOL function is expecting a ".db package" to be named as the second argument.

And I would actually recommend that you consider using the (hopefully more useful) new select() method.  Which you should be able to call like this:

select(hugene10stprobeset.db, keys = ids, cols = c("SYMBOL", "GENENAME"))


  Marc



----- Original Message -----
From: "Stephen Turner" <vustephen at gmail.com>
To: bioconductor at r-project.org
Sent: Monday, January 16, 2012 1:57:56 PM
Subject: [BioC] limma topTable with gene symbols in output: annotate problem

I ran an analysis analyses using limma on some Affy HuGene 1.0 ST arrays
(i.e. "HuGene-1_0-st-v1" in the @cdfName slot of the affybatch). I want to
output gene symbols with topTable, and I'm trying to follow these
instructions using the annotate package:
https://stat.ethz.ch/pipermail/bioconductor/2009-October/029908.html

I loaded the environments hugene10stv1cdf and hugene10stprobeset.db from
http://www.bioconductor.org/packages/release/data/annotation/

If "probeids" is the ID column from the topTable output, when I try getting
to the gene symbols using getSYMBOL(probeids, "hugene10stprobeset.db"),
every probe ID comes back NA. When I try using getSYMBOL(probeids,
"hugene10stv1cdf"), I get a nasty error:

Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
ifnotfound = NA) :
  error in evaluating the argument 'envir' in selecting a method for
function 'mget': Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
  object 'hugene10stv1cdfSYMBOL' not found

I realize that I could probably use biomaRt to annotate my results, but I
was hoping to do this quickly using one of the annotation files.

How would I most easily output toptable results with gene names (GO terms,
gene descriptions, etc) attached?

Thanks,

Stephen

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