Question: Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
14.7 years ago by
Ken Termiso • 250
Ken Termiso • 250 wrote:
Hi Sean, Maybe from now on I'll just email you directly instead of the mailing list :) Thanks for your reply...I did something similar to get what I wanted and I think it's pretty simple (provided you're using the affy annotation file): Say I wanted to get a list of all genes related to cell death: # "ann" is a data frame containing the affy annotation file HG-U133A_2_annot_csv.zip off their website i <- grep("death", as.vector(ann$Gene.Ontology.Biological.Process)) j <- grep("apoptosis", as.vector(ann$Gene.Ontology.Biological.Process)) k <- union(i,j) k <- sort(k) #optional, but the union arg returns unsorted te <- data.frame() te <- ann[k,] Now "te" is a data frame that contains the genes that have either "death" or "apoptosis" mentioned in GO Biol. Proc. I see there in your reply that you are using the annotate library -- the only annotation I've used is the affy file, which contains a lot of fields -- do you recommend using the annotate library over this? I've been using the affy file b/c it's a simple .csv file and thus is pretty straightforward to work with in R. Thanks again, Ken >From: Sean Davis <email@example.com> >To: "Ken Termiso" <firstname.lastname@example.org> >CC: email@example.com >Subject: Re: [BioC] Anyone have a GO slim list for Affy HG-U133A or >HG-U133Av2? Date: Thu, 24 Feb 2005 12:47:57 -0500 > >Ken, > >You could certainly produce such a list by repeating what they have done on >that website. For example, for GO_slim, biologic process 3 (cell cycle and >proliferation): > >library(hgu133a) >library(annotate) >genes <- >unlist(lookUp(c('GO:0007049','GO:0008283'),'hgu133a','GO2ALLPROBES')) >genes <- genes[!duplicated(genes)] > >This will contain the genes in cell cycle and proliferation. It wouldn't >be hard to automate this process for each category. For those categories >that include EXCLUDE descriptions, you can use R set commands like %in% to >get the sets you want. > >Sean > >On Feb 24, 2005, at 11:44 AM, Ken Termiso wrote: > >>Hi, >> >>I'm using the affy HG-U133A_2_annot_csv.zip annotation file to annotate my >>data (which may be a bad idea to begin with..?), and would like to be able >>to use the GO slim categories to annotate my data (see >>http://www.spatial.maine.edu/~mdolan/MGI_GO_Slim.html), instead of the >>extremely detailed GO categories already present in the affymetrix file - >>Gene.Ontology.Biological.Process, Gene.Ontology.Cellular.Component, >>Gene.Ontology.Molecular.Function. >> >>Basically, the issue is that I don't want to have the 2,000 - 5,000 >>different annotation groups in my file. I want to be able to run subset() >>on very general groups, like "development" or "death". >> >>Thanks in advance, >>Ken >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >
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