Hello all, I'm trying to use the overlapper.R script to calculate Venn
intersections between gene lists. Apparently there is a lot of user error,
as I cannot get any output. Here is what I am doing. 

 

1.       Start R 2.9.0

2.       Start the script:
>source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/ove
rLapper.R")

3.       Define the setlist:  > setlist <- list(A=sample(letters, 2707),
B=sample(letters, 3812), C=sample(letters, 1215), D=sample(letters, 943),
E=sample(letters, 4320, replace=T))

4.       Copy the Excel data into the clipboard.

5.       Read the data into R: > read.delim("clipboard", header=F) 

a.       Sample input

4318      NA      NA      NA      NA 7650653

4319      NA      NA      NA      NA 7650725

4320      NA      NA      NA      NA 7650735

 

6.       Calculate the Venn overlaps: > OLlist <-
overLapper(setlist=setlist, sep="", type="vennsets"); OLlist; names(OLlist)

 

But the array data appears to be empty, since I can output a file but no
overlaps between the sets. The export file has the possible overlaps, but no
probeID's.Help? J

 

 

 

- Brian

 


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