GeneSetCollection using EntrezID
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@javier-perez-florido-3121
Last seen 6.0 years ago
Dear list, I would like to carry out a Gene Set Analysis on the KEGG pathways on my Human Gene ST 1.0 array experiment using GSEABase. The annotation data included in this experiment is pd.hugene.1.0.st.v1, but it hasn't got functions like pd.hugene.1.0.st.v1PATH2PROBE. These functions are handled by hugene10sttranscriptcluster.db, so, my idea was to, first, using hugene10sttranscriptclusterENTREZID to get the entrezID for each gene in the experiment and then call GeneSetCollection using these entrezIDs, something like that: GeneSetCollection(entrezIDlist, idType="EntrezIdentifier",setType=KEGGCollection()), but it doesn't work Error en function (classes, fdef, mtable) : unable to find an inherited method for function "GeneSetCollection", for signature "character", "character", "KEGGCollection" How can I build my Gene set object? Thanks, Javier
Annotation Pathways GSEABase Annotation Pathways GSEABase • 1.4k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
Hi Javier -- Javier P?rez Florido <jpflorido at="" gmail.com=""> writes: > Dear list, > I would like to carry out a Gene Set Analysis on the KEGG pathways on > my Human Gene ST 1.0 array experiment using GSEABase. The annotation > data included in this experiment is pd.hugene.1.0.st.v1, but it hasn't > got functions like pd.hugene.1.0.st.v1PATH2PROBE. These functions are > handled by hugene10sttranscriptcluster.db, so, my idea was to, first, > using hugene10sttranscriptclusterENTREZID to get the entrezID for each > gene in the experiment and then call GeneSetCollection using these > entrezIDs, something like that: > > GeneSetCollection(entrezIDlist, > idType="EntrezIdentifier",setType=KEGGCollection()), but it doesn't > work > Error en function (classes, fdef, mtable) : > unable to find an inherited method for function "GeneSetCollection", > for signature "character", "character", "KEGGCollection" Are you looking for something like the following from the help page for GeneSetCollection? ## from KEGG identifiers, for example library(KEGG.db) lst <- head(as.list(KEGGEXTID2PATHID)) gsc <- GeneSetCollection(mapply(function(geneIds, keggId) { GeneSet(geneIds, geneIdType=EntrezIdentifier(), collectionType=KEGGCollection(keggId), setName=keggId) }, lst, names(lst))) but perhaps with lst <- head(as.list(KEGGEXTID2PATHID)) replaced by lst <- as.list(KEGGEXTID2PATHID[entrezIDlist]) Martin > > How can I build my Gene set object? > Thanks, > Javier > > _______________________________________________ > 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 M1 B861 Phone: (206) 667-2793
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Using read.affy() one ends up with an AffyBatch, a complex R structure. If, at that point, you decide you want to run RMA on a subset of the chips you just read in, things get tricky -- you are definitely not dealing with a matrix whose columns you can simply reference at will. In the past, I have dealt with this by simply starting over. This makes me feel like sort of an idiot. Is there a nice way to create a modified AffyBatch containing only the chips I want? Thanks. Tom
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With the affydata package installed, data(Dilution) loads an AffyBatch instance "Dilution"; Dilution[,1:3] is a three-chip subset; the class is closed under the subsetting operation so this yields a valid AffyBatch. The interpretation of "[,]" applied to AffyBatch instances should be intuitive _for indices provided to the right of the comma_. If you have something to the left of the comma, you will get a warning; there the interpretation is not intuitive but reflects ancient legacy. If you are seeing something different provide all details. On Fri, Nov 20, 2009 at 5:48 AM, Thomas Hampton < Thomas.H.Hampton@dartmouth.edu> wrote: > Using read.affy() one ends up with an AffyBatch, a complex R structure. If, > at that point, you decide > you want to run RMA on a subset of the chips you just read in, things get > tricky -- you are definitely > not dealing with a matrix whose columns you can simply reference at will. > > In the past, I have dealt with this by simply starting over. This makes me > feel like sort of an idiot. > > Is there a nice way to create a modified AffyBatch containing only the > chips I want? > > Thanks. > > Tom > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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