Peng Yu wrote: > Hi, > > I still run into other problems with the following fixes. Can some > more experienced BioC user help update these files and post them on > BioC website? All new users will appreciate your help! To follow the book verbatim, use R version 2.4 and correctly installed Bioconductor packages (i.e., appropriate for R 2.4, as provided by biocLite()). For a more recent treatment of similar material see http://bioconductor.org/pub/biocases/. For the problem below, see ?xtable and "An Introduction to R", for instance section 10.9 (hint: invoke as xtable(gcMat, ...) but take the time to understand why this works. Martin > > Regards, > Peng > > On Sun, Aug 9, 2009 at 7:30 AM, Heidi Dvinge<heidi at="" ebi.ac.uk=""> wrote: >> Hello Peng, >> >> please keep discussions to the list, so that other people can chime in as >> well. >> >> I'm not familiar with the details of xtable, but in the example you link >> to below it seems like the function xtable.matrix() does exist, but it's >> not exported by the name space. However, simply using xtable() works fine >> for me, and gives the same result at calling xtable.matrix() specifically >> (code shown below). >> >> There might be an updated version of the examples from "Bioinformatics and >> Computational Biology Solutions Using R and Bioconductor" somewhere; >> someone else can probably tell you. My best advice though is, that when >> something doesn't work, simply do a search for that function/package ;) >> Typing ?xtable.matrix gives you the xtable help page, which a.o. says "The >> available method functions for xtable are given by methods(xtable)." >> >> Regards >> \Heidi >> >>> library(GO.db) >>> library(xtable) >>> methods(xtable) >> [1] xtable.anova* xtable.aov* xtable.aovlist* >> xtable.coxph* >> [5] xtable.data.frame* xtable.glm* xtable.lm* >> xtable.matrix* >> [9] xtable.prcomp* xtable.summary.aov* >> xtable.summary.aovlist* xtable.summary.glm* >> [13] xtable.summary.lm* xtable.summary.prcomp* xtable.table* >> xtable.ts* >> [17] xtable.zoo* >> >> Non-visible functions are asterisked >>> goTerms <- contents(GOTERM) >>> goCats <- sapply(goTerms, Ontology) >>> gCnums <- table(goCats)[c("BP","CC", "MF")] >>> gCmat <- matrix(as.integer(gCnums), dimnames=list(c("BP","CC","MF"), >> "Number of terms")) >>> xtable.matrix(gCmat, display=c("d","d"), caption="Number of GO terms >> per ontology.", label="ta:GOprops") >> Error: could not find function "xtable.matrix" >>> xtable:::xtable.matrix(gCmat, display=c("d","d"), caption="Number of GO >> terms per ontology.", label="ta:GOprops") >> % latex table generated in R 2.9.0 by xtable 1.5-5 package >> % Sun Aug 9 13:17:48 2009 >> \begin{table}[ht] >> \begin{center} >> \begin{tabular}{rr} >> \hline >> & Number of terms \\ >> \hline >> BP & 16067 \\ >> CC & 2297 \\ >> MF & 8506 \\ >> \hline >> \end{tabular} >> \caption{Number of GO terms per ontology.} >> \label{ta:GOprops} >> \end{center} >> \end{table} >>> xtable(gCmat, display=c("d","d"), caption="Number of GO terms per >> ontology.", label="ta:GOprops") >> % latex table generated in R 2.9.0 by xtable 1.5-5 package >> % Sun Aug 9 13:17:59 2009 >> \begin{table}[ht] >> \begin{center} >> \begin{tabular}{rr} >> \hline >> & Number of terms \\ >> \hline >> BP & 16067 \\ >> CC & 2297 \\ >> MF & 8506 \\ >> \hline >> \end{tabular} >> \caption{Number of GO terms per ontology.} >> \label{ta:GOprops} >> \end{center} >> \end{table} >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-apple-darwin8.11.1 >> >> locale: >> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] xtable_1.5-5 GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 >> AnnotationDbi_1.6.0 >> [6] Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] tools_2.9.0 >> >> >> >> >>> Hi Heidi, >>> >>> I have figured out how to change the package names. But there are >>> still some command that is not running, for example 'xtable.matrix' in >>> the script that I pointed out in my orginal post. >>> >>> Could you please take a look how to correct these commands? >>> >>> Regards, >>> Peng >>> >>> On Sun, Aug 9, 2009 at 2:58 AM, Heidi Dvinge<heidi at="" ebi.ac.uk=""> wrote: >>>> Hi Peng, >>>> >>>> in general, all the annotation package now have an ".db" ending to >>>> reflect >>>> an underlying change to a database structure. In this particular case >>>> you'd therefore want GO.db, but the same would apply to e.g. KEGG.db, >>>> and >>>> all the chip annotation packages (moe430a.db, hgu133a.db, >>>> mogene10stprobeset.db etc.). >>>> >>>> Please see >>>> http://www.bioconductor.org/packages/release/AnnotationData.html for all >>>> the annotation packages. >>>> >>>> Best >>>> \Heidi >>>> >>>> >>>>> Hi, >>>>> >>>>> The examples in "Bioinformatics and Computational Biology Solutions >>>>> Using R and Bioconductor" are outdated. For example, I don't find the >>>>> package "GO" in >>>>> http://www.bioconductor.org/mogr/chapter-code/metaOverview.R >>>>> >>>>> I'm wondering if somebody can help updated the examples to reflect the >>>>> changes in BioC in the last 4 years. >>>>> >>>>> Regards, >>>>> Peng >>>>> >>>>> _______________________________________________ >>>>> 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 -- 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