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 [[alternative HTML version deleted]]

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]