Hello All,

Once again I am seeking the help of this forum. I am making an R package that streamlines my microarray analysis. It is driving me mad. I have 4 main functions at work, I try to combine them into one. Individually they work but together I get the following error.

Error in topTable(normfit, number = 1e+05, adjust = "BH", lfc = 1) : 
  fit must be an MArrayLM object

The problem which I think is happening, since each function uses an input of what comes before it , the 3rd function does not complete running before the last one starts.

function (mydir, group, design, contrast) 
{
    lonoan(mydir)
    filterc(normData)
    normfit(normData, group, design, contrast)
    results(normfit)
}

The error comes from my results function.

function (normfit) 
{
    probeset.list <- topTable(normfit, number = 1e+05, adjust = "BH", 
        lfc = 1)
    Symbol <- getSYMBOL(rownames(probeset.list), "hugene20sttranscriptcluster.db")
    results <- cbind(probeset.list, Symbol)
    assign("results", results, envir = .GlobalEnv)
}

At the end of the run the normfit variable is in the global environment and if I run the function again it works. This is driving me mad. Any solutions? Thanks.