note that read.table creates a data.frame instance (see ?read.table, Value
section).  As far as I can tell, DGEList will
succeed with such an input although it explicitly asks for a matrix in its
help page.  Therefore the most likely issue is that you have some nonnumeric
data in a column of your seq_data.  You will need to spend some time with R
documentation to become more independent with interpreting error messages.
Please do read the bioconductor mailing list posting guide.



On Wed, Sep 7, 2011 at 7:36 PM, Khan, Saad M. (MU-Student) <
smk5g5@mail.missouri.edu> wrote:

> Hi I am a novice in both R and EdgeR. I have a readcounts tab seperated
> file (with around 24 conditions belonging to 6 different groups  with its
> first column containing the tag identifiers and the other columns containing
> the read counts. I used read.delim function in R in the following manner :-
>
>
>
> seq_data <- read.table("newfile.txt", header = TRUE, sep = "\t" )
>
>
>
> after that I tried to make a DGEList in the following manner :-
>
>
>
>  Dlist <- DGEList (counts = seq_data)
>
>
>
> it gives me the following error :-
>
>
>
> Error in colSums(counts) : 'x' must be numeric
>
>
>
> after going through the mailing list i also tried the solution given below
> in one of the mailing list :-
>
>
>
> for (f in seq_data$files)
>
>    str(read.delim(f, stringAsFactors=FALSE))
>
>
>
> but it does not works. Please suggest where I am going wrong
>
>
>
> thanks & regards
>
> Saad
>
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>
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