[BioC] error calculating alpha in edgeR

[Mark Robinson]

Hi Milena.

Small oversight on my part.  If you use 'as.matrix(mydata)' in place of
'mydata', you should have no problems.  This is imposed on the data matrix
in the next version (which might take a day or so to come online).

A couple of other small points:

1. You may want to use the new constructor (instead of creating the list
yourself):

d<-DGEList(data=y,group=grouping,lib.size=lib_size)

2. In terms of analysis of differential expression, there may not be much
value in the rows of your table that have VERY low counts (e.g. your
100134814_100136947).  In the past, I've noticed some instabilities in the
NB calculations with very low counts and I've generally filtered out the
rows with (say) 3 or less total counts.

Cheers,
Mark



> 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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