Dear gurus, I have recently hit upon the following problem whilst using the getURL method of the annaffy package: The method works fine when my aafGO object is of length > 1: > ann.affy.go[[4]] An object of class "aafGO" [[1]] An object of class "aafGOItem" @id "GO:0000139" @name "Golgi membrane" @type "Cellular Component" @evid "IEA" [[2]] An object of class "aafGOItem" @id "GO:0003827" @name "alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity" @type "Molecular Function" @evid "IEA" [[3]] An object of class "aafGOItem" @id "GO:0006487" @name "protein amino acid N-linked glycosylation" @type "Biological Process" @evid "IEA" > getURL(ann.affy.go[[4]]) [1] "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=query&que ry=GO:0000139%0aGO:0003827%0aGO:0006487" The problem arises when using aafGO objects of length==1: > ann.affy.go[[37]] An object of class "aafGO" [[1]] An object of class "aafGOItem" @id "GO:0016787" @name "hydrolase activity" @type "Molecular Function" @evid "IEA" > getURL(ann.affy.go[[37]]) Error in object[[i]] : subscript out of bounds This is easily solved by checking length(ann.affy.go[[x]]) and further sub-setting the object: > getURL(ann.affy.go[[37]][[1]]) [1] "http://amigo.geneontology.org/cgi- bin/amigo/go.cgi?view=details&query=GO:0016787" What I am wondering, is if there is a better way to cope with these situations. This seems to be something that I come across over and over again when writing R code. Accessing elements of a matrix which changes within some for loop, always involves some fumbling to check that the matrix has not collapsed into a vector, that can no longer be accessed using mat[3,1], since for that instance the data is now vec[3]. Do people have a standard way to cope with such situations? Thank you in advance, Ana -- Ana P. C. Rodrigues, Ph.D. Salk Institute for Biological Studies T +1 858.453.4100 x1983 W bioinformatics.salk.edu/people/ana/

On Jan 30, 2008, at 10:27 AM, Ana Rodrigues wrote: > Dear gurus, > I have recently hit upon the following problem whilst using the getURL > method of the annaffy package: > > The method works fine when my aafGO object is of length > 1: > >> ann.affy.go[[4]] > An object of class "aafGO" > [[1]] > An object of class "aafGOItem" > @id "GO:0000139" > @name "Golgi membrane" > @type "Cellular Component" > @evid "IEA" > > [[2]] > An object of class "aafGOItem" > @id "GO:0003827" > @name "alpha-1,3-mannosylglycoprotein > 2-beta-N-acetylglucosaminyltransferase activity" > @type "Molecular Function" > @evid "IEA" > > [[3]] > An object of class "aafGOItem" > @id "GO:0006487" > @name "protein amino acid N-linked glycosylation" > @type "Biological Process" > @evid "IEA" > >> getURL(ann.affy.go[[4]]) > [1] "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi? > view=query&query=GO:0000139%0aGO:0003827%0aGO:0006487" > > > The problem arises when using aafGO objects of length==1: > >> ann.affy.go[[37]] > An object of class "aafGO" > [[1]] > An object of class "aafGOItem" > @id "GO:0016787" > @name "hydrolase activity" > @type "Molecular Function" > @evid "IEA" > >> getURL(ann.affy.go[[37]]) > Error in object[[i]] : subscript out of bounds > > This is easily solved by checking length(ann.affy.go[[x]]) and further > sub-setting the object: > >> getURL(ann.affy.go[[37]][[1]]) > [1] "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi? > view=details&query=GO:0016787" > > > What I am wondering, is if there is a better way to cope with these > situations. > > This seems to be something that I come across over and over again when > writing R code. > Accessing elements of a matrix which changes within some for loop, > always involves some fumbling to check that the matrix has not > collapsed into a vector, that can no longer be accessed using > mat[3,1], since for that instance the data is now vec[3]. For this problem you can use matrix subsetting like [,,drop = FALSE] which will always return a vector, say tmp = matrix(1:9,3,3) tmp[1,] # a vector tmp[1,,drop = false] # a 1x3 matrix Kasper > Do people have a standard way to cope with such situations? > Thank you in advance, > Ana > > -- > Ana P. C. Rodrigues, Ph.D. > Salk Institute for Biological Studies > T +1 858.453.4100 x1983 > W bioinformatics.salk.edu/people/ana/ > > _______________________________________________ > 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

Dear Ana, you could use drop=FALSE when subsetting your matrix/ dataframe to pevent collapsing to vectors: mar[1:4,1,drop=FALSE] will retain the dimensions of the matrix Best Florian Florian Hahne Computational Biolology Group Fred Hutchinson Cancer Research Center, Seattle fhahne at fhrcr.org On 30.01.2008, at 13:27, "Ana Rodrigues" <arodrigues at="" salk.edu=""> wrote: > Dear gurus, > I have recently hit upon the following problem whilst using the getURL > method of the annaffy package: > > The method works fine when my aafGO object is of length > 1: > >> ann.affy.go[[4]] > An object of class "aafGO" > [[1]] > An object of class "aafGOItem" > @id "GO:0000139" > @name "Golgi membrane" > @type "Cellular Component" > @evid "IEA" > > [[2]] > An object of class "aafGOItem" > @id "GO:0003827" > @name "alpha-1,3-mannosylglycoprotein > 2-beta-N-acetylglucosaminyltransferase activity" > @type "Molecular Function" > @evid "IEA" > > [[3]] > An object of class "aafGOItem" > @id "GO:0006487" > @name "protein amino acid N-linked glycosylation" > @type "Biological Process" > @evid "IEA" > >> getURL(ann.affy.go[[4]]) > [1] "http://amigo.geneontology.org/cgi- bin/amigo/go.cgi?view=query&query=GO:0000139%0aGO:0003827%0aGO:0006487 > " > > > The problem arises when using aafGO objects of length==1: > >> ann.affy.go[[37]] > An object of class "aafGO" > [[1]] > An object of class "aafGOItem" > @id "GO:0016787" > @name "hydrolase activity" > @type "Molecular Function" > @evid "IEA" > >> getURL(ann.affy.go[[37]]) > Error in object[[i]] : subscript out of bounds > > This is easily solved by checking length(ann.affy.go[[x]]) and further > sub-setting the object: > >> getURL(ann.affy.go[[37]][[1]]) > [1] "http://amigo.geneontology.org/cgi- bin/amigo/go.cgi?view=details&query=GO:0016787 > " > > > What I am wondering, is if there is a better way to cope with these > situations. > > This seems to be something that I come across over and over again when > writing R code. > Accessing elements of a matrix which changes within some for loop, > always involves some fumbling to check that the matrix has not > collapsed into a vector, that can no longer be accessed using > mat[3,1], since for that instance the data is now vec[3]. > > Do people have a standard way to cope with such situations? > Thank you in advance, > Ana > > -- > Ana P. C. Rodrigues, Ph.D. > Salk Institute for Biological Studies > T +1 858.453.4100 x1983 > W bioinformatics.salk.edu/people/ana/ > > _______________________________________________ > 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