How can I make genesets for sigpathway
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@srinivas-iyyer-939
Last seen 6.5 years ago
Dear group, in sigPathway package, authors used muscle data. when one loads: library(sigPathway) data(MuscleExample) I see a "G" object which is nothing but a lit of all genes. > G[1] [[1]] [[1]]$src [1] "GO:0030054" [[1]]$title [1] "cell junction" [[1]]$probes [1] "220519_s_at" "206083_at" "204455_at" "212253_x_at" I get clueless in R with list operations. How can I make my own sets mimicking "G" list object. Thank you . srini ________________________________________________________________ ____________________ Be a better friend, newshound, and sigPathway sigPathway • 454 views ADD COMMENTlink 0 Entering edit mode @james-w-macdonald-5106 Last seen 12 hours ago United States Hi Srini, Srinivas Iyyer wrote: > Dear group, > in sigPathway package, authors used > muscle data. > > when one loads: > library(sigPathway) > data(MuscleExample) > I see a "G" object which is nothing but a lit of all > genes. > >> G[1] > [[1]] > [[1]]$src > [1] "GO:0030054" > > [[1]]$title > [1] "cell junction" > > [[1]]$probes > [1] "220519_s_at" "206083_at" "204455_at" > "212253_x_at" > > > I get clueless in R with list operations. > > How can I make my own sets mimicking "G" list object. Well, it depends on what you are starting with. Do you have an Affy chip? Illumina? Did you roll yer own? Without knowing where you are starting I don't think anybody can help you. Also note that the authors seem to have a bunch of these lists already made that you can download from their site. Have you looked there to see if they already made what you want? Best, Jim > > Thank you . > srini > > > ______________________________________________________________ ______________________ > Be a better friend, newshound, and > > _______________________________________________ > 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
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Dear Jim , thanks for your input. For now I am using U133Plus2 and Later I will be using affy and agilent mouse and rat chips respectively. Although, I found the site where they are describing how to make "G" object, the script that was provided is not straightforward and I get errors when I am trying to process what the author is asking me to do.( http://www.chip.org/~ppark/Supplements/PNAS05.html) My ultimate aim is to combine my choice of datasets: some from MsigDB, my own annotations, PPI sets etc. into "G"list object. For that the starting material I have is a TAB delim file with: Pathway Source Name of Pathway GENE symbols. Now I am clueless as how to create a annotation list. This is required to start doing what authors are describing in their code how to convert gene symbols to ID. Simply, I dont know how to make an object equivalent to "Genesets_EntrezGeneIDs.RData". "Genesets_EntrezGeneIDs.RData" is an R workspace containing Entrez GeneIDs corresponding to gene sets from GO, KEGG, and other pathway databases. egidDir <- getwd() > egidDir [1] "C:/Documents and Settings/srini/My Documents/software" >load(file.path(egidDir, "Genesets_EntrezGeneIDs.RData")) > biocAnnot <- "rat2302" > library(biocAnnot, character.only = TRUE) Error in library(biocAnnot, character.only = TRUE) : there is no package called 'rat2302' > biocAnnot [1] "rat2302" > ls() [1] "biocAnnot" "egidDir" "G.EGIDs" > xx <- as.list(get(paste(biocAnnot, "ENTREZID", sep = ""))) Error in get(paste(biocAnnot, "ENTREZID", sep = "")) : > sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] sigPathway_1.6.0 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 This might be as simple stupid question as how to make lists in R. But truly lists is one of my nightmares. Thanks Srini --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Hi Srini, > > Srinivas Iyyer wrote: > > Dear group, > > in sigPathway package, authors used > > muscle data. > > > > when one loads: > > library(sigPathway) > > data(MuscleExample) > > I see a "G" object which is nothing but a lit of > all > > genes. > > > >> G[1] > > [[1]] > > [[1]]$src > > [1] "GO:0030054" > > > > [[1]]$title > > [1] "cell junction" > > > > [[1]]$probes > > [1] "220519_s_at" "206083_at" "204455_at" > > "212253_x_at" > > > > > > I get clueless in R with list operations. > > > > How can I make my own sets mimicking "G" list > object. > > Well, it depends on what you are starting with. Do > you have an Affy > chip? Illumina? Did you roll yer own? > > Without knowing where you are starting I don't think > anybody can help you. > > Also note that the authors seem to have a bunch of > these lists already > made that you can download from their site. Have you > looked there to see > if they already made what you want? > > Best, > > Jim > > > > > > Thank you . > > srini > > > > > > > ______________________________________________________________________ ______________ > > Be a better friend, newshound, and > > > > _______________________________________________ > > 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 > ________________________________________________________________ ____________________ Be a better friend, newshound, and ADD REPLYlink 0 Entering edit mode Hi Srini, Srinivas Iyyer wrote: > Dear Jim , > thanks for your input. > For now I am using U133Plus2 and Later I will be > using affy and agilent mouse and rat chips > respectively. > > Although, I found the site where they are describing > how to make "G" object, the script that was provided > is not straightforward and I get errors when I am > trying to process what the author is asking me to do.( > http://www.chip.org/~ppark/Supplements/PNAS05.html) > > > My ultimate aim is to combine my choice of datasets: > some from MsigDB, my own annotations, PPI sets etc. > into "G"list object. > > For that the starting material I have is a TAB delim > file with: > > Pathway Source Name of Pathway GENE symbols. > > > Now I am clueless as how to create a annotation list. > This is required to start doing what authors are > describing in their code how to convert gene symbols > to ID. > > Simply, I dont know how to make an object equivalent > to "Genesets_EntrezGeneIDs.RData". > > "Genesets_EntrezGeneIDs.RData" is an R workspace > containing Entrez GeneIDs corresponding to gene sets > from GO, KEGG, and other pathway databases. Well, I think this will be way too complicated for anyone to help you with via a listserv. > > > > > > egidDir <- getwd() >> egidDir > [1] "C:/Documents and Settings/srini/My > Documents/software" > >> load(file.path(egidDir, > "Genesets_EntrezGeneIDs.RData")) >> biocAnnot <- "rat2302" >> library(biocAnnot, character.only = TRUE) > Error in library(biocAnnot, character.only = TRUE) : > there is no package called 'rat2302' So the error ^^^^^^^^^^^^ right there indicates you don't have this package installed yet. >> biocAnnot > [1] "rat2302" >> ls() > [1] "biocAnnot" "egidDir" "G.EGIDs" >> xx <- as.list(get(paste(biocAnnot, "ENTREZID", sep = > ""))) > Error in get(paste(biocAnnot, "ENTREZID", sep = "")) : Since the package isn't installed, you will not be able to get anything from it. Anyway, if you want to do something this complicated (e.g., not just using the sigPathways package as intended) then you will likely have to get help from the authors to make your own G.EGIDs list. On the webpage you reference at the bottom it says to contact Peter J. Park if you have questions. I think probably that is the best way to go. Best, Jim > >> sessionInfo() > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United > States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] sigPathway_1.6.0 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 tools_2.6.1 > > > This might be as simple stupid question as how to make > lists in R. But truly lists is one of my nightmares. > > Thanks > Srini > > > > > > > > > > > --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > wrote: > >> Hi Srini, >> >> Srinivas Iyyer wrote: >>> Dear group, >>> in sigPathway package, authors used >>> muscle data. >>> >>> when one loads: >>> library(sigPathway) >>> data(MuscleExample) >>> I see a "G" object which is nothing but a lit of >> all >>> genes. >>> >>>> G[1] >>> [[1]] >>> [[1]]$src >>> [1] "GO:0030054" >>> >>> [[1]]$title >>> [1] "cell junction" >>> >>> [[1]]$probes >>> [1] "220519_s_at" "206083_at" "204455_at" >>> "212253_x_at" >>> >>> >>> I get clueless in R with list operations. >>> >>> How can I make my own sets mimicking "G" list >> object. >> >> Well, it depends on what you are starting with. Do >> you have an Affy >> chip? Illumina? Did you roll yer own? >> >> Without knowing where you are starting I don't think >> anybody can help you. >> >> Also note that the authors seem to have a bunch of >> these lists already >> made that you can download from their site. Have you >> looked there to see >> if they already made what you want? >> >> Best, >> >> Jim >> >> >>> Thank you . >>> srini >>> >>> >>> > ____________________________________________________________________ ________________ >>> Be a better friend, newshound, and >>> >>> _______________________________________________ >>> 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 >> > > > > ______________________________________________________________ ______________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > -- 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