Agnes, Thanks for clering that up for me. I had been trying to yank some data files out of .rda packages to see how they might be formatted and to practice the demo examples but extracting components from .rda's has been, for me, another nosebleed entirely. I will give this a try with the GOids I have and try to figure out a way to use my spots annotated with GO id's to work with some of these functions while maintaining GOid-transcript labelling for the output. Wish me luck. Your advice will help a great deal. Cheers, -Adlai On Aug 15, 2005, at 10:03 PM, Paquet, Agnes wrote: > Hi Adlai, > > goTools functions are expecting a list of lists of oligo ids as input, > either affymetrix, operon or GO ids. goTools will only recognize these > 3 types of ids. > > Some example of inputs are provided in the example dataset probeID and > in the goTools overview. > > To take a look at the example dataset: > library(goTools) > data(probeID) > operonlist > > You can use read.table to read your ascii file into R, then create > your list of lists using subsets. For example, if you want to compare > two groups of oligo ids, with each group stored in a separate text > file with one oligo id by line, you can create your list by typing: > > group1 <- read.table("Group1.txt", sep="\n") > group2 <- read.table("Group2.txt", sep="\n") > myList <- list(G1=as.character(group1[,1]), > G2=as.character(group2[,1])) > ontoCompare(myList, probeType="correct probeType") > > You can also refer to ?read.table for more details about how to read > in an ascii file. > > Best, > > Agnes > > ________________________________ > > From: bioconductor-bounces at stat.math.ethz.ch on behalf of adlai burman > Sent: Mon 8/15/2005 2:17 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] goTools data formatting > > > > Can anyone tell me either: > How to format an ascii file for data input for use with goTools > functions, or > Where I can find file formatting specs? > > I am not using affy data but high density microarray data which are > annotated with genbank IDs, GO annotations, tanscript names and common > transcript symbols. > > Thanks in advance, > Adlai > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >