[BioC] GOstats gene set size selection

[alex lam (RI)]

Dear colleagues,

I have been following the GOstats vignette to test GO terms association.
I would like to know whether it is possible to set limits on the number
of selected genes in GO term and the size of that term on my affy chip?

For example, can I tell hyperGTest to skip testing a GO term if the
number of significant genes in that term is under, say, 3, or if there
are more than 400 genes of that GO term on the chip? 

Currently I found many of my significant GO terms not very specific. As
I am trying to incorporate GOstats to an expression QTL (eQTL) genome
scan, I get a lot of output. Therefore, ideally I would like to filter
out these terms before test rather than screening the results after
test. Is there such an option with hyperGTest?

Many thanks for your advice,
Alex

   > sessionInfo()
R version 2.6.2 Patched (2008-03-24 r44882)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID
ENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] GOstats_2.4.0       Category_2.4.0      genefilter_1.16.0
 [4] survival_2.34       RBGL_1.14.0         annotate_1.16.1
 [7] xtable_1.5-2        GO.db_2.0.2         AnnotationDbi_1.0.6
[10] RSQLite_0.6-8       DBI_0.2-4           Biobase_1.16.3
[13] graph_1.16.1

loaded via a namespace (and not attached):
[1] cluster_1.11.10
>

--------------------------------------------
Alex C. Lam
Roslin Institute (Edinburgh)
Midlothian
EH25 9PS
United Kingdom
Tel: +44 131 5274471

Former email address: alex.lam at bbsrc.ac.uk
New email address: alex.lam at roslin.ed.ac.uk
Both addresses are functional

Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity (registered
number SC023592). Our registered office is at Roslin, Midlothian, EH25
9PS. VAT registration number 847380013.

The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of the addressee only.   The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute