Hi, I'm writing with a questions that follows up on a previous correspondence I had within this mailing list (copied below). Essentially I'm trying to use ontoTools to ge a mapping between the union of the probe sets on the HGU95 av2, b, c, d, e and GO biological process terms. To this end, I've first created an environment, named hgu95GO, which was defined as described below, using parent.env, following a suggestion by R. Gentleman: > hgu95GO<-hgu95av2GO > parent.env(hgu95GO)<-hgu95bGO > parent.env(hgu95bGO)<-hgu95cGO > parent.env(hgu95cGO)<-hgu95dGO) > parent.env(hgu95dGO)<-hgu95eGO For this we have > length(ls(env=hgu95GO)) [1] 12625 which is the same as the length for hgu95av2GO, rather then the length of the union of the 5 probe set collections from av2 to e (which is 62906). However if I look for a value of a key corresponding to a probe set from b, c,... indeed it gives me something by looking at the parent. I'm not too familiar with environments in R, but I guess this is the expected behavior. Now, I've built a mapping: ooMapHgu952GOBP<-otkvEnv2namedSparse(obs, tms, hgu95GO) where tms are the nodes of a go biological process graph that I've built and obs is ls(env=hgu95GO). I'm concerned though that since the latter seems to be equal to ls(env=hgu95av2) only, I'm not getting the mapping that I desired from the union of all *5* collections of probe sets on the 5 Affy chips to my GO BP terms and indeed if I run: > ooc.Hgu95.GOBP<-makeOOC(goBPonto, ooMapHgu952GOBP) > print(OOmap(ooc.Hgu95.GOBP)) named sparse matrix of dim[1] 12625 7807 the first dimension is 12625, not 62906. Am I correct in my interpretation that I'm not getting what I was seeking? If so, how can I get around it? I.e. what would be the quickest way to build a mapping from the union of the probe sets on the 5 Affy Chips to my Go BP ontology? Thanks for any help you might give me, Elisabetta On Wed, 17 Dec 2003, Elisabetta Manduchi wrote: > > Robert, > thank you very much for such a prompt reply. > A question, with your notation below, shouldn't I do my gets on E5 rather > than on E1, if E1 is the ancestor? Was that a just typo or am I > misunderstanding? > In other words to deal with my case, I guess I could do the following > (calling hgu95GO my new combined environment): > > hgu95GO<-hgu95av2GO > parent.env(hgu95GO)<-hgu95bGO > parent.env(hgu95bGO)<-hgu95cGO > parent.env(hgu95cGO)<-hgu95dGO) > parent.env(hgu95dGO)<-hgu95eGO > > and then do my gets on hgu95GO, right? > Elisabetta > > On Wed, 17 Dec 2003, Robert Gentleman wrote: > > > On Wed, Dec 17, 2003 at 03:47:54PM -0500, Elisabetta Manduchi wrote: > > > > > > Hi, > > > I would like to create an environment that combines the hgu95av2GO, > > > hgu95bGO, ...hgu95eGO into just one environment, that I can subsequently > > > use as the otkvEnv argument in the ontoTools function otkvEnv2namedSparse. > > > Is there a quick and simple way to do this in R, without having to define > > > a new hash and the key-value mapping block by block (according to which > > > environment the key belongs to)? In other words, I'm asking if there is a > > > one-stop way in R to "union" the above 5 environments. > > > > Sort of, in R there are no hash tables but environments are close so > > we used them. They have a rather unique aspect which is the parent > > environment. So that if a value is not found in the first environment > > the parent is searched. So to solve your problem you could do some > > thing like > > > > parent.env(E2) <- E1 > > parent.env(E3) <- E2 > > ... > > > > then do your get's on E1 (with inherits=TRUE, which is the default > > in get) and you should be almost set. The one issue that is not > > easily solved is the if inherits is TRUE then you search up beyond > > the last of your environments (your work space and then the search > > list). But that should not be a problem in your case.... > > > > Robert > > > > > Thanks, > > > Elisabetta > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > -- Elisabetta Manduchi Computational Biology and Informatics Laboratory Center for Bioinformatics University of Pennsylvania 1428 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104-6021 phone: 215-573-4408 fax: 215 573-3111 email: manduchi@pcbi.upenn.edu web: http://www.cbil.upenn.edu/~manduchi ---

Hi, I'm writing with a questions that follows up on a previous correspondence I had within this mailing list (copied below). Essentially I'm trying to use ontoTools to ge a mapping between the union of the probe sets on the HGU95 av2, b, c, d, e and GO biological process terms. To this end, I've first created an environment, named hgu95GO, which was defined as described below, using parent.env, following a suggestion by R. Gentleman: > hgu95GO<-hgu95av2GO > parent.env(hgu95GO)<-hgu95bGO > parent.env(hgu95bGO)<-hgu95cGO > parent.env(hgu95cGO)<-hgu95dGO) > parent.env(hgu95dGO)<-hgu95eGO For this we have > length(ls(env=hgu95GO)) [1] 12625 which is the same as the length for hgu95av2GO, rather then the length of the union of the 5 probe set collections from av2 to e (which is 62906). However if I look for a value of a key corresponding to a probe set from b, c,... indeed it gives me something by looking at the parent. I'm not too familiar with environments in R, but I guess this is the expected behavior. Now, I've built a mapping: ooMapHgu952GOBP<-otkvEnv2namedSparse(obs, tms, hgu95GO) where tms are the nodes of a go biological process graph that I've built and obs is ls(env=hgu95GO). I'm concerned though that since the latter seems to be equal to ls(env=hgu95av2) only, I'm not getting the mapping that I desired from the union of all *5* collections of probe sets on the 5 Affy chips to my GO BP terms and indeed if I run: > ooc.Hgu95.GOBP<-makeOOC(goBPonto, ooMapHgu952GOBP) > print(OOmap(ooc.Hgu95.GOBP)) named sparse matrix of dim[1] 12625 7807 the first dimension is 12625, not 62906. Am I correct in my interpretation that I'm not getting what I was seeking? If so, how can I get around it? I.e. what would be the quickest way to build a mapping from the union of the probe sets on the 5 Affy Chips to my Go BP ontology? Thanks for any help you might give me, Elisabetta On Wed, 17 Dec 2003, Elisabetta Manduchi wrote: > > Robert, > thank you very much for such a prompt reply. > A question, with your notation below, shouldn't I do my gets on E5 rather > than on E1, if E1 is the ancestor? Was that a just typo or am I > misunderstanding? > In other words to deal with my case, I guess I could do the following > (calling hgu95GO my new combined environment): > > hgu95GO<-hgu95av2GO > parent.env(hgu95GO)<-hgu95bGO > parent.env(hgu95bGO)<-hgu95cGO > parent.env(hgu95cGO)<-hgu95dGO) > parent.env(hgu95dGO)<-hgu95eGO > > and then do my gets on hgu95GO, right? > Elisabetta > > On Wed, 17 Dec 2003, Robert Gentleman wrote: > > > On Wed, Dec 17, 2003 at 03:47:54PM -0500, Elisabetta Manduchi wrote: > > > > > > Hi, > > > I would like to create an environment that combines the hgu95av2GO, > > > hgu95bGO, ...hgu95eGO into just one environment, that I can subsequently > > > use as the otkvEnv argument in the ontoTools function otkvEnv2namedSparse. > > > Is there a quick and simple way to do this in R, without having to define > > > a new hash and the key-value mapping block by block (according to which > > > environment the key belongs to)? In other words, I'm asking if there is a > > > one-stop way in R to "union" the above 5 environments. > > > > Sort of, in R there are no hash tables but environments are close so > > we used them. They have a rather unique aspect which is the parent > > environment. So that if a value is not found in the first environment > > the parent is searched. So to solve your problem you could do some > > thing like > > > > parent.env(E2) <- E1 > > parent.env(E3) <- E2 > > ... > > > > then do your get's on E1 (with inherits=TRUE, which is the default > > in get) and you should be almost set. The one issue that is not > > easily solved is the if inherits is TRUE then you search up beyond > > the last of your environments (your work space and then the search > > list). But that should not be a problem in your case.... > > > > Robert > > > > > Thanks, > > > Elisabetta > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > -- Elisabetta Manduchi Computational Biology and Informatics Laboratory Center for Bioinformatics University of Pennsylvania 1428 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104-6021 phone: 215-573-4408 fax: 215 573-3111 email: manduchi@pcbi.upenn.edu web: http://www.cbil.upenn.edu/~manduchi ---

I think I found an easy solution to the question I had posed below. Namely I was setting obs<-ls(env=hgu95GO) which limited my observations to the 12625 probe sets on av2. By resetting obs<-hgu95.probeset where the latter is the union of the probesets for all 5 chips and then proceeding as before: > ooMapHgu952GOBP<-otkvEnv2namedSparse(obs, tms, hgu95GO) things seem to work as desired. Sorry if I wasted anybody's time on this question. Elisabetta On Mon, 12 Jan 2004, Elisabetta Manduchi wrote: > > Hi, > I'm writing with a questions that follows up on a previous correspondence > I had within this mailing list (copied below). > Essentially I'm trying to use ontoTools to ge a mapping between the union > of the probe sets on the HGU95 av2, b, c, d, e and GO biological process > terms. > To this end, I've first created an environment, named hgu95GO, which was > defined as described below, using parent.env, following a suggestion by R. > Gentleman: > > > hgu95GO<-hgu95av2GO > > parent.env(hgu95GO)<-hgu95bGO > > parent.env(hgu95bGO)<-hgu95cGO > > parent.env(hgu95cGO)<-hgu95dGO) > > parent.env(hgu95dGO)<-hgu95eGO > > For this we have > > > length(ls(env=hgu95GO)) > [1] 12625 > > which is the same as the length for hgu95av2GO, rather then the length of > the union of the 5 probe set collections from av2 to e (which is 62906). > However if I look for a value of a key corresponding to a probe set from > b, c,... indeed it gives me something by looking at the parent. I'm not > too familiar with environments in R, but I guess this is the expected > behavior. Now, I've built a mapping: > > ooMapHgu952GOBP<-otkvEnv2namedSparse(obs, tms, hgu95GO) > > where tms are the nodes of a go biological process graph that I've built > and obs is ls(env=hgu95GO). > I'm concerned though that since the latter seems to be equal to > ls(env=hgu95av2) only, I'm not getting the mapping that I desired from > the union of all *5* collections of probe sets on the 5 Affy chips to my > GO BP terms and indeed if I run: > > > ooc.Hgu95.GOBP<-makeOOC(goBPonto, ooMapHgu952GOBP) > > print(OOmap(ooc.Hgu95.GOBP)) > named sparse matrix of dim[1] 12625 7807 > > the first dimension is 12625, not 62906. Am I correct in my > interpretation that I'm not getting what I was seeking? If so, how can I > get around it? I.e. what would be the quickest way to build a mapping from > the union of the probe sets on the 5 Affy Chips to my Go BP ontology? > Thanks for any help you might give me, > Elisabetta > > On Wed, 17 Dec 2003, Elisabetta Manduchi wrote: > > > > > Robert, > > thank you very much for such a prompt reply. > > A question, with your notation below, shouldn't I do my gets on E5 rather > > than on E1, if E1 is the ancestor? Was that a just typo or am I > > misunderstanding? > > In other words to deal with my case, I guess I could do the following > > (calling hgu95GO my new combined environment): > > > > hgu95GO<-hgu95av2GO > > parent.env(hgu95GO)<-hgu95bGO > > parent.env(hgu95bGO)<-hgu95cGO > > parent.env(hgu95cGO)<-hgu95dGO) > > parent.env(hgu95dGO)<-hgu95eGO > > > > and then do my gets on hgu95GO, right? > > Elisabetta > > > > On Wed, 17 Dec 2003, Robert Gentleman wrote: > > > > > On Wed, Dec 17, 2003 at 03:47:54PM -0500, Elisabetta Manduchi wrote: > > > > > > > > Hi, > > > > I would like to create an environment that combines the hgu95av2GO, > > > > hgu95bGO, ...hgu95eGO into just one environment, that I can subsequently > > > > use as the otkvEnv argument in the ontoTools function otkvEnv2namedSparse. > > > > Is there a quick and simple way to do this in R, without having to define > > > > a new hash and the key-value mapping block by block (according to which > > > > environment the key belongs to)? In other words, I'm asking if there is a > > > > one-stop way in R to "union" the above 5 environments. > > > > > > Sort of, in R there are no hash tables but environments are close so > > > we used them. They have a rather unique aspect which is the parent > > > environment. So that if a value is not found in the first environment > > > the parent is searched. So to solve your problem you could do some > > > thing like > > > > > > parent.env(E2) <- E1 > > > parent.env(E3) <- E2 > > > ... > > > > > > then do your get's on E1 (with inherits=TRUE, which is the default > > > in get) and you should be almost set. The one issue that is not > > > easily solved is the if inherits is TRUE then you search up beyond > > > the last of your environments (your work space and then the search > > > list). But that should not be a problem in your case.... > > > > > > Robert > > > > > > > Thanks, > > > > Elisabetta > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@stat.math.ethz.ch > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > > > -- Elisabetta Manduchi Computational Biology and Informatics Laboratory Center for Bioinformatics University of Pennsylvania 1428 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104-6021 phone: 215-573-4408 fax: 215 573-3111 email: manduchi@pcbi.upenn.edu web: http://www.cbil.upenn.edu/~manduchi ---