[BioC] limma2biomaRt error

Mayte Suarez-Farinas farinam at mail.rockefeller.edu
Tue Oct 23 16:05:54 CEST 2007


I installed R 6.0 and BioC Packages. I got an error in lima2biomaRt
function of package affycoretools:

Checking attributes and filters ... ok
Error in missing(affy.attr) : 'missing' can only be used for arguments

but neither in the help nor in the  function parameters there is one  
called affy.attr.
I checked the function and there is a call to limma2biomaRt.n with  
this parameter.
see below.

limma2biomaRt
function (eset, fit, design, contrast, species, links = linksBM()[1:3],
     otherdata = annBM()[1:3], ann.source = "entrezgene", adjust =  
"fdr",
     number = 30, pfilt = NULL, fldfilt = NULL, tstat = TRUE,
     pval = TRUE, FC = TRUE, expression = TRUE, html = TRUE, text =  
TRUE,
     save = FALSE, addname = NULL, interactive = TRUE, affyid = FALSE,
     mysql = TRUE)
{
     if (!interactive) {
         limma2biomaRt.na(eset = eset, fit = fit, design = design,
             contrast = contrast, species = species, links = links,
             otherdata = otherdata, ann.source = ann.source, adjust =  
adjust,
             number = number, pfilt = pfilt, fldfilt = fldfilt,
             tstat = tstat, pval = pval, FC = FC, expression =  
expression,
             html = html, save = save, addname = addname, affyid =  
affyid,
             mysql = mysql, affy.attr = affy.attr)



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