[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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