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
On 7-Jan-10, at 7:30 AM, yupu wrote:
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
--
When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of
sessionInfo() and traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------
______________________________________________________________________
The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of the
sender.
______________________________________________________________________
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en