[BioC] goTools data formatting

[Paquet, Agnes]

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

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