Hi all, I have (again) some problems to use the package ath1121501. I don't understand the difference between ath1121501G02PROBE and ath1121501GO2ALLPROBES... I made a list listGO2GENE to have for each term GO all the genes that belong to this term GO. For this, I use ath1121501G02PROBE or ath1121501GO2ALLPROBES. The problem is that the result depends on the choice between ath1121501G02PROBE or ath1121501GO2ALLPROBES. For example, if I use ath1121501G02PROBE, listGO2GENE["GO:0008104"] gives me three genes in the the GO term GO:0008104 $"GO:0008104" [1] "AT1G48090" "AT3G50380" "AT5G24740" and if I use ath1121501GO2ALLPROBES, I obtain more than 570 genes for this GO term... So what is the right file I have to use to obtain the list that gives me all the genes (in TAIR format) for a particular GO term. Here under, I give you the code I used to obtain the list listGO2GENE...may be the pb is in my code??But it corresponds to a part of the code GOHyperG, so it would be right... goV<-mget(ls(ath1121501GO2PROBE),ath1121501GO2PROBE) listGO2GENE<- sapply(goV, function(x) { if (length(x) == 0 || is.na(x)) return(NA) lls <- unique(unlist(mget(x, get("ath1121501LOCUSID",mode="environment")))) lls <- lls[!is.na(lls)] lls }) Thanks for your help, Olivier.

Hi Martin, Martin Olivier <martinol at="" ensam.inra.fr=""> writes: > I have (again) some problems to use the package ath1121501. > I don't understand the difference between ath1121501G02PROBE and > ath1121501GO2ALLPROBES... Here's the description from the help pages of those two environments: ath1121501GO2PROBE is an R environment that provides mappings between GO identifiers and manufacturer identifiers. ath1121501GO2ALLPROBES is an R environment that provides mappings between a given GO identifier and all manufactuerer identifiers annotated at that GO term or one of its children in the GO ontology. > I made a list listGO2GENE to have for each term GO all the genes that belong > to this term GO. For this, I use ath1121501G02PROBE or > ath1121501GO2ALLPROBES. The problem is that the result depends on the choice > between ath1121501G02PROBE or ath1121501GO2ALLPROBES. Since the two environments are different, is this a problem? ;-) > For example, if I use ath1121501G02PROBE, listGO2GENE["GO:0008104"] gives me > three genes in the the GO term GO:0008104 > $"GO:0008104" > [1] "AT1G48090" "AT3G50380" "AT5G24740" > > and if I use ath1121501GO2ALLPROBES, I obtain more than 570 genes > for this GO term... > > So what is the right file I have to use to obtain the list that gives me > all the genes > (in TAIR format) for a particular GO term. It depends a bit on what you want, but I think you want the *GO2ALLPROBES environment. This one says, given GO term X, give me all the probe set IDs annotated at X or at a term that is a descendant of X. That is the real annotation list for GO term X. > Here under, I give you the code I used to obtain the list > listGO2GENE...may be > the pb is in my code??But it corresponds to a part of the code GOHyperG, > so it > would be right... > > goV<-mget(ls(ath1121501GO2PROBE),ath1121501GO2PROBE) as.list(someEnv) would be easier here. > listGO2GENE<- sapply(goV, function(x) { > if (length(x) == 0 || is.na(x)) > return(NA) Not sure this part does what you want. The x may have length > 1 in which case you return NA for x = c(NA, foo, bar, baz), but not for x = c(foo, bar, NA, baz). You probably want: if (length(x) == 0 || (length(x) == 1 && is.na(x))) > lls <- unique(unlist(mget(x, > get("ath1121501LOCUSID",mode="environment")))) If you know the name of the env, there is no reason to use get(). > lls <- lls[!is.na(lls)] > lls > }) Also, FYI, GOstats has gone through a major revision in the 1.9 release; GOHyperG is deprecated in favor of hyperGTest (see the vignette). Also, you didn't tell us versions of anything and that would, in general, be helpful. + seth

> >I have (again) some problems to use the package ath1121501. >I don't understand the difference between ath1121501G02PROBE and >ath1121501GO2ALLPROBES... GO2PROBE gives you the probes that are associated with a given GO id. GO2ALLPROBES givens you the probes that associated with a given GO id + probes that associated with the GO ids that are the child-nodes of that GO id. > >I made a list listGO2GENE to have for each term GO all the genes that belong >to this term GO. For this, I use ath1121501G02PROBE or >ath1121501GO2ALLPROBES. The problem is that the result depends on the choice >between ath1121501G02PROBE or ath1121501GO2ALLPROBES. > >For example, if I use ath1121501G02PROBE, listGO2GENE["GO:0008104"] gives me >three genes in the the GO term GO:0008104 >$"GO:0008104" >[1] "AT1G48090" "AT3G50380" "AT5G24740" > >and if I use ath1121501GO2ALLPROBES, I obtain more than 570 genes >for this GO term... > >So what is the right file I have to use to obtain the list that gives me >all the genes >(in TAIR format) for a particular GO term. > > >Here under, I give you the code I used to obtain the list >listGO2GENE...may be >the pb is in my code??But it corresponds to a part of the code GOHyperG, >so it >would be right... > >goV<-mget(ls(ath1121501GO2PROBE),ath1121501GO2PROBE) >listGO2GENE<- sapply(goV, function(x) { > if (length(x) == 0 || is.na(x)) > return(NA) > lls <- unique(unlist(mget(x, >get("ath1121501LOCUSID",mode="environment")))) > lls <- lls[!is.na(lls)] > lls >}) > > >Thanks for your help, >Olivier. > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Martin Olivier wrote: > Hi all, > > I have (again) some problems to use the package ath1121501. > I don't understand the difference between ath1121501G02PROBE and > ath1121501GO2ALLPROBES... The difference is outlined in the help page for these two environments: ath1121501GO2PROBE is an R environment that provides mappings between GO identifiers and manufacturer identifiers. ath1121501GO2ALLPROBES is an R environment that provides mappings between a given GO identifier and all manufactuerer identifiers annotated at that GO term or one of its children in the GO ontology. So if you want to map from a GO term to a probe ID, you would likely want the GO2PROBE environment. Best, Jim > > I made a list listGO2GENE to have for each term GO all the genes that belong > to this term GO. For this, I use ath1121501G02PROBE or > ath1121501GO2ALLPROBES. The problem is that the result depends on the choice > between ath1121501G02PROBE or ath1121501GO2ALLPROBES. > > For example, if I use ath1121501G02PROBE, listGO2GENE["GO:0008104"] gives me > three genes in the the GO term GO:0008104 > $"GO:0008104" > [1] "AT1G48090" "AT3G50380" "AT5G24740" > > and if I use ath1121501GO2ALLPROBES, I obtain more than 570 genes > for this GO term... > > So what is the right file I have to use to obtain the list that gives me > all the genes > (in TAIR format) for a particular GO term. > > > Here under, I give you the code I used to obtain the list > listGO2GENE...may be > the pb is in my code??But it corresponds to a part of the code GOHyperG, > so it > would be right... > > goV<-mget(ls(ath1121501GO2PROBE),ath1121501GO2PROBE) > listGO2GENE<- sapply(goV, function(x) { > if (length(x) == 0 || is.na(x)) > return(NA) > lls <- unique(unlist(mget(x, > get("ath1121501LOCUSID",mode="environment")))) > lls <- lls[!is.na(lls)] > lls > }) > > > Thanks for your help, > Olivier. > > _______________________________________________ > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.