Question: help with ath1121501
0
gravatar for Martin Olivier
13.2 years ago by
Martin Olivier70 wrote:
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.
go ath1121501 • 438 views
ADD COMMENTlink modified 13.2 years ago by Seth Falcon7.4k • written 13.2 years ago by Martin Olivier70
Answer: help with ath1121501
0
gravatar for Seth Falcon
13.2 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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
ADD COMMENTlink written 13.2 years ago by Seth Falcon7.4k
Answer: help with ath1121501
0
gravatar for John Zhang
13.2 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
> >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
ADD COMMENTlink written 13.2 years ago by John Zhang2.9k
Answer: help with ath1121501
0
gravatar for James W. MacDonald
13.2 years ago by
United States
James W. MacDonald52k wrote:
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.
ADD COMMENTlink written 13.2 years ago by James W. MacDonald52k
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