Very clear. Thanks Marc. 2011/5/10 Marc Carlson <mcarlson at="" fhcrc.org="">: > Hi Alberto, > > So the way that the annotation packages work is that they take a probe to > gene mapping from a manufacturer and then return to you the relevant gene > information that is associated with the gene that is mapped to by a specific > probe. > > If there was no mapping between the probe and the gene provided by the > manufacturer, we have not attempted to guess one for you. > > But if you feel that you have better information about where these probes > map to (perhaps you took the time to align them to the genome and see what > genes are nearby as you did ?for this one here), then you could supply that > mapping to the SQLForge code in the AnnotationDbi package and produce a new > annotation package based on that. ?The details on how to do this are > described here in one of the vignettes from the AnnotationDbi package > > http://www.bioconductor.org/packages/2.8/bioc/vignettes/AnnotationDb i/inst/doc/SQLForge.pdf > > I hope this clarifies things, > > > ?Marc > > > > On 05/10/2011 05:34 AM, Alberto Goldoni wrote: >> >> @Davis >> >> You are right! But i have tryed to perform this kind of search: >> >> library("rgug4130a.db") >> x<- rgug4130aENSEMBL >> mapped_genes<- mappedkeys(x) >> xx<- as.list(x[mapped_genes]) >> >> or this approach: >> >> x<- rgug4130aGENENAME >> mapped_probes<- mappedkeys(x) >> xx<- as.list(x[mapped_probes]) >> >> but the results are the same in some genes there is:"unknown function". >> >> I would like to know if there is a method in order to perform the >> search using another database or directly to the Rat Genome Database >> or using biomaRt...but i don't know how. >> I have more or less 100 genes with an "unknown function" and it would >> be very useful if there is a script or function in order to perform >> automatically instead of serching genes one by one. >> >> >> Best regards. >> >> 2011/5/10 Sean Davis<sdavis2 at="" mail.nih.gov="">: >>> >>> On Tue, May 10, 2011 at 8:17 AM, Alberto Goldoni >>> <alberto.goldoni1975 at="" gmail.com=""> ?wrote: >>>> >>>> @Vincent >>>> >>>> The chip used is the "rgug4130a" so i have to use the "rgug4130a.db" >>>> database. >>>> >>>> In order to obtain the toptable this is my history: >>>> >>>> library(limma) >>>> library(vsn) >>>> targets<- readTargets("targets.txt") >>>> RG<- read.maimages(targets$FileName, source="agilent") >>>> MA<- normalizeBetweenArrays(RG, method="Aquantile") >>>> contrast.matrix<- >>>> >>>> >>>> cbind("(hda+str)-(ref)"=c(1,0),"(ref+str)-(ref)"=c(0,1),"(hda+str )-(ref+str)"=c(1,-1)) >>>> rownames(contrast.matrix)<- colnames(design) >>>> fit<- lmFit(MA, design) >>>> fit2<- contrasts.fit(fit, contrast.matrix) >>>> fit2<- eBayes(fit2) >>>> geni500<-topTable(fit2,number=500,adjust="BH") >>>> >>> Hi, Alberto. >>> The data in your topTable result are taken from the feature extraction >>> result file. ?In other words, rgug4130a.db is not used in what you show >>> above. ?You could add to your annotation using either rgug4130a.db or >>> biomaRt, but you will need to perform these steps yourself. ?As to why >>> some >>> of your probes do not appear to have annotation, you would probably need >>> to >>> contact Agilent as they are the source of your current annotation. >>> Hope that helps, >>> Sean >>> >>>>> sessionInfo() >>>> >>>> R version 2.12.1 (2010-12-16) >>>> Platform: i386-pc-mingw32/i386 (32-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United Kingdom.1252 ?LC_CTYPE=English_United >>>> Kingdom.1252 >>>> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C >>>> [5] LC_TIME=English_United Kingdom.1252 >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] AnnotationDbi_1.12.0 Biobase_2.10.0 ? ? ? limma_3.6.9 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] DBI_0.2-5 ? ? RSQLite_0.9-4 tools_2.12.1 >>>> >>>> >>>> >>>> 2011/5/10 Vincent Carey<stvjc at="" channing.harvard.edu="">: >>>>> >>>>> 1) you did not provide sessionInfo(), which is critical for helping >>>>> you to diagnose an issue that may pertain to software version -- >>>>> revisions to annotation packages can have all sorts of consequences >>>>> >>>>> 2) i am not sure rgug4130.db has anything to do with this. >>>>> >>>>>> get("CB606456", revmap(rgug4130aSYMBOL)) >>>>> >>>>> Error in .checkKeys(value, Rkeys(x), x at ifnotfound) : >>>>> ?value for "CB606456" not found >>>>> >>>>> >>>>> and so on. ?look at the featureData component of the object passed to >>>>> lmFit -- the annotation may be in there. ?if this does not give >>>>> clarification please give very explicity indication of how the >>>>> topTable was generated, going back to the structure of the object >>>>> passed to lmFit >>>>> >>>>> On Tue, May 10, 2011 at 5:30 AM, Alberto Goldoni >>>>> <alberto.goldoni1975 at="" gmail.com=""> ?wrote: >>>>>> >>>>>> Dear All, >>>>>> i'm analyzing agilent microarrays with the "rgug4130a.db" database and >>>>>> using the function:"topTable(fit2,number=500,adjust="BH")" i have >>>>>> obtained 500 genes like these: >>>>>> >>>>>> Row ? ? Col ? ? ProbeUID ? ? ? ?ControlType ? ? ProbeName >>>>>> GeneName ? ? ? ?SystematicName ?Description ? ? X.hda.str...ref. >>>>>> ?X.ref.str...ref. ? ? ? ?X.hda.str...ref.str. ? ?AveExpr F >>>>>> P.Value >>>>>> adj.P.Val >>>>>> 16096 ? 79 ? ? ?38 ? ? ?15309 ? 0 ? ? ? A_43_P10328 ? ? CB606456 >>>>>> ?CB606456 ? ? ? ?unknown >>>>>> function ? ? ? ?3.988290607 ? ? -0.951656306 ? ?4.939946913 >>>>>> 10.29735936 ? ? 36.77263264 ? ? 0.000212298 ? ? 0.641094595 >>>>>> 8109 ? ?40 ? ? ?109 ? ? 7609 ? ?0 ? ? ? A_42_P552092 ? ?203358_Rn >>>>>> 203358_Rn ? ? ? Rat c-fos >>>>>> mRNA. ? 5.670956889 ? ? 4.413365374 ? ? ? ?1.257591514 ? ? 13.47699544 >>>>>> ? ? 33.20342601 ? ? 0.000292278 ? ? 0.641094595 >>>>>> >>>>>> but as you can see most genes like the first one ?- CB606456 - ?in the >>>>>> DESCRPTION there is written "unknown function". >>>>>> >>>>>> So i have performed a very simply search. >>>>>> 1) First in ENSAMBLE using the GeneName "CB606456" with the "Locations >>>>>> of DnaAlignFeature" it gives to me the Genomic location(strand): chr >>>>>> 7:16261621-16262210 >>>>>> 2) Then in the Rat Genome Database >>>>>> (http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=735058) i have found >>>>>> that in this position there is one gene: >>>>>> >>>>>> 735058 ?GENE ? ?Angptl4 angiopoietin-like 4 ? ? 7 ? ? ? 16261623 >>>>>> ?16267852 >>>>>> >>>>>> so the question is why in the "rgug4130a.db" database the R system >>>>>> gives to me "unknown function" when using the genomic location in >>>>>> ensamble and then in rgd it gives to me the Angptl4 gene! >>>>>> >>>>>> and there is a function in order to do to R to perform this kind of >>>>>> search automatically? (this why in my 500 genes there are 100 "unknow >>>>>> function" genes and it will be interesting to have a function that >>>>>> perform this kind of search automatically). >>>>>> >>>>>> >>>>>> Best regards to all and to whom answer to me. >>>>>> >>>>>> -- >>>>>> ----------------------------------------------------- >>>>>> Dr. Alberto Goldoni >>>>>> Parma, Italy >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>> >>>> >>>> -- >>>> ----------------------------------------------------- >>>> Dr. Alberto Goldoni >>>> Parma, Italy >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ----------------------------------------------------- Dr. Alberto Goldoni Parma, Italy