Sebastien Gerega wrote: > Thanks for that! > I can now almost get what I want..... > Here is the code I use: > > hgOver = hyperGTest(params) > report = summary(hgOver, htmlLinks=TRUE) > cats = sigCategories(hgOver) > reportGenes = vector() > > for(i in 1:length(cats)){ > reportGenes = append(reportGenes, geneIdsByCategory(hgOver, cats[i])) > } > > This gives me reportGenes as a list something like this: > > $`04650` > [1] 10451 4277 5296 5880 6464 8743 8795 8797 > > $`04670` > [1] 10451 1365 5296 5829 5880 6387 6494 87 9564 > > $`00150` > [1] 3291 51451 6715 > > $`04080` > [1] 154 2150 4886 4923 7433 > > $`04360` > [1] 10512 1969 2043 56920 57522 57556 5880 6387 > > I would then like to run the following code: > > report <- data.frame(report, reportGenes) > xtab <- xtable(report, caption="A Caption") > print(xtab, type="html", file="Afile.html", caption.placement="top", > sanitize.text.function=function(x) x, include.rownames=FALSE) > > But I get the following error: > Error in data.frame("04650" = c(10451L, 4277L, 5296L, 5880L, 6464L, > 8743L, : > arguments imply differing number of rows: 8, 9, 3, 5, 7 This is the part where I said you have to wrap the Entrez Gene IDs in

EGID

so you can a.)have a vector of the correct length, and b.) create a table that will be readable. Something like this should suffice: rg.out <- sapply(reportGenes, function(x) paste("

", paste(x, collapse="

"), "

", sep="")) then use rg.out in lieu of reportGenes when making the data.frame. Best, Jim > > How should I deal with this list so that I can add it to the data.frame? > And are there any faster ways to do what I have done in this code? > I am still getting used to R. > thanks heaps, > Sebastien > > James W. MacDonald wrote: >> Hi Sebastien, >> >> Maybe not directly, but note that htmlReport() is simply using xtable >> to create the HTML page using the output from summary(). So you could >> just create the table and then add a column of Entrez Gene IDs and >> then output the result. >> >> Say your GOHyperGResult object is called 'hypt': >> >> out <- summary(hyp, summary.args=list(htmlLinks=TRUE, categorySize=10)) >> >> Note that the categorySize argument isn't necessary, but does protect >> you from choosing arguably spurious results (like a GO term with 3 >> genes in the universe and 1 that was significant). >> >> Now you are going to have to create a vector containing all the Entrez >> Gene IDs for each GO term. For this to work in HTML, you will also >> need to separate each ID with a

EntreGeneID

, so you will need >> to either cat() or paste() things together. Once you have that, just >> add to the data.frame created above: >> >> out <- data.frame(out, entregeneidvector) >> xtab <- xtable(out, caption="A Caption", digits=rep(c(3,0), c(4,8))) >> print(xtab, type="html", file="A file name.html", >> caption.placement="top", sanitize.text.function=function(x) x, >> include.rownames=FALSE) >> >> HOWEVER, that might not really be what you want, as it will obviously >> be a bit of work, and could get really messy if there are dozens of >> Entrez Gene IDs for a particular GO term. An alternative is to output >> individual HTML tables for each GO term of interest that list out the >> probesets that contributed to the significance of that term. For that >> you might want to look at hyperGoutput() in the affycoretools package. >> >> Best, >> >> Jim >> >> >> Sebastien Gerega wrote: >>> Hi, >>> is there any way to get additional information into the hyperGTest >>> html report? >>> Specifically, I would like to include the Entrez IDs for the genes >>> contributing to >>> each overrepresented GO term. >>> thanks, >>> Sebastien >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623