[BioC] Gostats with Yeast annotation
alexg at ruggedtextile.com
Fri Jul 25 10:35:30 CEST 2008
Just to confirm the org.Sc.sgd.db package and GOstats seem to work
fine together for me in Bioc-devel (Sample session pasted below).
R version 2.8.0 Under development (unstable) (2008-07-22 r46103)
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[Previously saved workspace restored]
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: graph
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: GO.db
Loading required package: RBGL
> sel = readLines("Turbidostat.genes")
> uni = readLines("all.genes")
> params =
> over = hyperGTest(params)
GOBPID Pvalue OddsRatio ExpCount Count Size
GO:0006412 GO:0006412 1.109223e-16 2.755286 62.1352567 125 383
GO:0010467 GO:0010467 4.482367e-14 1.824627 225.8284001 317 1392
GO:0009059 GO:0009059 8.256804e-14 2.232463 89.0659423 154 549
GO:0043170 GO:0043170 8.691113e-13 1.698656 414.6676658 510 2556
GO:0044267 GO:0044267 5.484817e-12 1.746362 214.3098539 296 1321
GO:0019538 GO:0019538 1.268805e-11 1.718287 224.6927688 306 1385
Save workspace image? [y/n/c]: n
ag357 at ag357-pc2102:~/Desktop/study> head Turbidostat.genes
ag357 at ag357-pc2102:~/Desktop/study> head all.genes
On 22 Jul 2008, at 18:07, Robert Gentleman wrote:
> Hi Alex,
> If you are willing to use R-devel and Bioc-devel, the issue should
> be fixed there. I would be interested in hearing of any problems
> you might have (or successes) using that version. I am waiting for
> some reports of success before I port this to release,
> best wishes
> Alex Gutteridge wrote:
>> I've been trying to use the hyperGTest method from the GOstats
>> package with some yeast ORF data. I notice in this thread from a
>> month or so ago that there are problems at the moment with using
>> any of the yeast annotation sets apart from 'YEAST' (which is
>> deprecated) due to missing ID2EntrezID methods:
>> I just wanted to make sure that this was still the case and I guess
>> fish around for an estimated ETA for when the org.Sc.sgd.db
>> annotations (which are replacing YEAST as I understand it) will be
>> compatible with hyperGTest?
>> Also, is the exact source of GO annotations used in these packages
>> documented anywhere? Looking in the DESCRIPTION file I see
>> 'primarily based on mapping using ORF identifiers from SGD' for
>> org.Sc.sgd.db and 'assembled using data from public data
>> repositories' for YEAST. Should I just take it these are based on
>> the SGD GO annotation file from the date given in the Packaged
>> field of the DESCRIPTION file? For YEAST there is
> the man page is pretty explicit, (?org.Sc.sgdGO)
> Mappings were based on data provided by: Yeast Genome (
> ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on
> I am not sure what more we could put there.
> best wishes
>> also a Created field which is aprox. 1 month prior to the Packaged
>> date so I'm guessing the real age of the data is that one? The
>> yeast annotations change so quickly it's useful to be able to pin
>> this down as accurately as possible.
>> Thanks in advance for any help with these questions.
>> Alex Gutteridge
>> Department of Biochemistry
>> University of Cambridge
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> rgentlem at fhcrc.org
Department of Biochemistry
University of Cambridge
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