[BioC] Gostats with Yeast annotation

[Alex Gutteridge]

Hi,

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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ISBN 3-900051-07-0
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[Previously saved workspace restored]
 > library(Category)
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
 > library(GOstats)
Loading required package: GO.db
Loading required package: RBGL
 > sel = readLines("Turbidostat.genes")
 > uni = readLines("all.genes")
 > params =  
new 
("GOHyperGParams 
",geneIds 
= 
sel 
,universeGeneIds 
= 
uni 
,annotation 
= 
"org 
.Sc 
.sgd 
.db 
",ontology="BP",pvalueCutoff=0.1,conditional=FALSE,testDirection="over")
 > over = hyperGTest(params)
 > summary(over)
               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
[..snip..]
 > q()
Save workspace image? [y/n/c]: n
ag357 at ag357-pc2102:~/Desktop/study> head Turbidostat.genes
YAL001C
YAL002W
YAL003W
YAL005C
YAL008W
YAL009W
YAL010C
YAL011W
YAL019W
ag357 at ag357-pc2102:~/Desktop/study> head all.genes
YHR047C
YHR051W
YHR066W
YHR068W
YHR075C
YHR076W
YHR080C
YHR083W
YHR143W-A
YKL137W

AlexG

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
>  Robert
>
>
> Alex Gutteridge wrote:
>> Hi,
>> 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:
>> https://stat.ethz.ch/pipermail/bioconductor/2008-June/022697.html
>> 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
>     2008-Mar29
>
> I am not sure what more we could put there.
>
> best wishes
>  Robert
>
>> 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
>> _______________________________________________
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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
> -- 
> 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
> 206-667-7700
> rgentlem at fhcrc.org
>

Alex Gutteridge

Department of Biochemistry
University of Cambridge