Hello, Is there any functions in bioconductor that can take an ExpressionSet, find the correct annotation object and then get information? So the function would use annotation() to get the object and then use that object for a specific purpose I have two uses for this: 1) Given a REFSEQ ID find the corresponding probes in an ExpressionSet and print the expression for those probes e.g. getExprFromREFSEQ(REFSEQID, ExpressionSet) 2) Given a probe and ExpressionSet find the gene symbol. getSymbol(ExpressionSet, ProbeID) If not, any ideas on the best way to do this? Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

On Wed, May 21, 2008 at 7:47 AM, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> wrote: > Hello, > > Is there any functions in bioconductor that can take an ExpressionSet, > find the correct annotation object and then get information? So the > function would use annotation() to get the object and then use that > object for a specific purpose > > I have two uses for this: > 1) Given a REFSEQ ID find the corresponding probes in an ExpressionSet > and print the expression for those probes e.g. > getExprFromREFSEQ(REFSEQID, ExpressionSet) > 2) Given a probe and ExpressionSet find the gene symbol. > getSymbol(ExpressionSet, ProbeID) > > If not, any ideas on the best way to do this? There are not functions for this, I do not think. However, you could, in a pretty straightforward way, write a function to extract the annotation slot (when it has something in it--it is not guaranteed to be non-NULL), load the appropriate annotation package if it exists, and then do the lookups you want. Or is there some other detail that I am missing from your post? Sean

Hi Daniel -- Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes: > No you are not missing anything. I thought this was a useful feature > and so probably some one had done it before and submitted it to > bioconductor, that is normally the case. I will just have to code it > myself. GSEABase does this kind of operation, for instance > library(GSEABase) > data(sample.ExpressionSet) > gs <- GeneSet(sample.ExpressionSet) > gs setName: NA geneIds: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (total: 500) geneIdType: Annotation (hgu95av2) collectionType: ExpressionSet details: use 'details(object)' > mapIdentifiers(gs, SymbolIdentifier()) setName: NA geneIds: STAT1, GAPDH, ..., OBSCN (total: 344) geneIdType: Symbol (hgu95av2) collectionType: ExpressionSet details: use 'details(object)' You can retrieve the mapped ids with the accessor geneIds(). In the reverse direction: > refseqIds [1] "NM_003747" "NM_007315" "NM_139266" "NP_003738" "NP_009330" "NP_644671" > gs <- GeneSet(refseqIds, geneIdType=RefseqIdentifier()) > gs setName: NA geneIds: NM_003747, NM_007315, ..., NP_644671 (total: 6) geneIdType: Refseq collectionType: Null details: use 'details(object)' > es <- sample.ExpressionSet[gs,] > es ExpressionSet (storageMode: lockedEnvironment) assayData: 8 features, 26 samples element names: exprs, se.exprs phenoData sampleNames: A, B, ..., Z (26 total) varLabels and varMetadata description: sex: Female/Male type: Case/Control score: Testing Score featureData featureNames: 31473_s_at, 31474_r_at, ..., AFFX- HUMISGF3A/M97935_MB_at (8 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: hgu95av2 you could then use exprs(es) to retrieve the expression values of the corresponding probes. Note the map between geneIds and features is not 1:1 in either direction. Martin > Dan > > Sean Davis wrote: >> On Wed, May 21, 2008 at 7:47 AM, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> wrote: >>> Hello, >>> >>> Is there any functions in bioconductor that can take an ExpressionSet, >>> find the correct annotation object and then get information? So the >>> function would use annotation() to get the object and then use that >>> object for a specific purpose >>> >>> I have two uses for this: >>> 1) Given a REFSEQ ID find the corresponding probes in an ExpressionSet >>> and print the expression for those probes e.g. >>> getExprFromREFSEQ(REFSEQID, ExpressionSet) >>> 2) Given a probe and ExpressionSet find the gene symbol. >>> getSymbol(ExpressionSet, ProbeID) >>> >>> If not, any ideas on the best way to do this? >> >> There are not functions for this, I do not think. However, you could, >> in a pretty straightforward way, write a function to extract the >> annotation slot (when it has something in it--it is not guaranteed to >> be non-NULL), load the appropriate annotation package if it exists, >> and then do the lookups you want. Or is there some other detail that >> I am missing from your post? >> >> Sean > > -- > ************************************************************** > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > Email: daniel.brewer at icr.ac.uk > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the a...{{dropped:2}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793