questiones about annotations for exon arrays: no gene symbol or refseq id for majority of core probe sets?

[yupu]

Hi,

I am new to exon array analysis. I managed to follow the instructions
from http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis
to get the estimation of transcript:

trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)

Then I followed the following thread's idea of using biomaRt to get
the annotation information through the group id of trFit object:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1f4af7fca4352022/a3fe6980ffa7b925?lnk=gst&q=questions+about+annotations#a3fe6980ffa7b925

groupnames = trFit[,2]

ann<-getBM(attributes = c("affy_huex_1_0_st_v2", "hgnc_symbol"),
filters = "affy_huex_1_0_st_v2", values = groupnames, mart = ensembl)

What surprised me is a majority of these group ids don't have any gene
symbol or refseq id associated with them (even I was using the core
probeset upstream)

> length(groupnames)
[1] 18708

>dim(ann)
[1] 7835 2

I am not sure if this is expected or I am doing something wrong here.

Thanks,
Yupu

[Mark Robinson]

Hi Yupu.

I haven't explored this in any detail, but on a cursory inspection
(below), it appears that biomaRt has 244000 probesets represented in
its database (which seems about right).

> bm <-
getBM
(attributes
=
c
("affy_huex_1_0_st_v2
","hgnc_symbol","chromosome_name","band"),mart=mart)
> dim(bm)
[1] 324334 4
> head(bm)
affy_huex_1_0_st_v2 hgnc_symbol chromosome_name band
1 3581777 IGHA2 14 q32.33
2 3581646 IGHA2 14 q32.33
3 3581642 IGHA2 14 q32.33
4 3581781 IGHA2 14 q32.33
5 3581783 IGHA2 14 q32.33
6 3581788 IGHA2 14 q32.33
> length(unique(bm$affy_huex_1_0_st_v2))
[1] 244801

Strictly speaking, this isn't an aroma.affymetrix question. What I
suggest you try is exploring what identifiers are not represented in
the database and whether something is missing from biomaRt (or the
Ensembl web page).

Of course, you can also get annotation from other sources (e.g. from
Affymetrix).

Hope that helps,
Mark

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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.rob...@garvan.org.au
e: mrob...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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