Question: Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
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14.7 years ago by
Ken Termiso250
Ken Termiso250 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 <sdavis2@mail.nih.gov> >To: "Ken Termiso" <jerk_alert@hotmail.com> >CC: bioconductor@stat.math.ethz.ch >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 >
modified 14.7 years ago by Aedin Culhane310 • written 14.7 years ago by Ken Termiso250
Answer: Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
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14.7 years ago by
Aedin Culhane310
Aedin Culhane310 wrote:
Dear Ken I was recently doing the same kind of this. I needed to get counts of genes in go slim classes on an old Affy hu6800 chip and compare this to the distribution of genes in the genome. To get GO slim counts I did the following library(annaffy) library(hu6800) # I got a listing of the GO Slim classes from the Integr8 website at EBI. # http://www.ebi.ac.uk/integr8/GOAnalysisPage.do?orgProteomeID=25 and saved this and a comma # separated file genome.go<-read.csv( "GO_count_ebi_integr8.csv") add.counts<-function(xx.list, ref){ n = length(ref) out=vector() for (i in 1:n) { go= as.character(ref[i]) if(length(xx.list) > 0){ go.count= length(xx.list[go][[1]]) out[i] = go.count } } return(out) } res.go$hu68002allprobe = add.counts(as.list(hu6800GO2ALLPROBES), genome.go[,1]) res.go$hu68002probe = add.counts(as.list(hu6800GO2PROBE), genome.go[,1]) Otherwise, you may wish to browse the equivalent to as.list(hu6800GO2ALLPROBES) as.list(hu6800GO2PROBE) The library(hgu133a_2) will have an equivalent hgu133a_2GO2ALLPROBES etc Hope this helps Aedin
Hi, I have a bunch of .INT files. I wrote a python script to chop the header information and other outlier probe information from a CEL file and I wrote only the intensities from CEL files to .INT files. Now my aim is to collect all the intensities from these 100 INT files and write a matrix. I wrote a small function, that goes to a directory picks up all the .INT files and write a matrix. I could not write this properly. Could any one correct me. Function: > cycle<-function(file.path=".",file.pattern="*.int") + { + files.2.process<-dir(path=file.path,pattern=file.pattern) + forfile.name in files.2.process) + { + current.file<-read.delimfile.name,sep='\t') + { + my_data<-data.frame(current.file) + } + } + } > data<-cycle("C:\Documents and Settings\Marray-affy\Database\U133\Bronchial_Epithelia\int\",".int") Error: syntax error Please help me. thanks S.Peri