[BioC] error calculating alpha in edgeR

Milena Gongora m.gongora at imb.uq.edu.au
Tue Sep 30 07:54:59 CEST 2008


Dear edgeR developers and users,

Just started using edgeR with next generation sequence (count) data.
When calculating alpha, I am getting the following error:

alpha <- alpha.approxeb(d)              
[quantileAdjust] Iteration (dot=1000) 1 :Error in y1/matrix(rep(1, 
nrow(y1)), ncol = 1) %*% lib.size1 :
  non-numeric argument to binary operator

I can't work out why I am getting this... any ideas?
Thanks!

The full code is below:
--------------
mydata <- read.table("myFile.txt", header=TRUE, row.names="ID")
head(mydata)
                            A.REP1 A.REP2 B.REP1 B.REP2
100011872_100012727_-       0       0       0       2
100017569_100017878_-       1       0       0       0
100134814_100136947_-       0       0       0       0
100134931_100136947_-       0       2       0       0
100137054_100138100_-       1       0       0       1
100137831_100138100_-       1       0       0       0

grouping <- c(1,1,2,2)
lib_size <- as.numeric(apply(mydata,2,sum))
lib_size
[1] 352812 573571 401573 719698

d <- new("DGEList", list(data=mydata, group=grouping, lib.size=lib_size))
alpha <- alpha.approxeb(d) 
[quantileAdjust] Iteration (dot=1000) 1 :Error in y1/matrix(rep(1, 
nrow(y1)), ncol = 1) %*% lib.size1 :
  non-numeric argument to binary operator
---------------------

-- 
Milena



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