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)

Hi Mayte, Thanks for the bug report - this is what happens when you try to back changes out, and you don't get all of them... I have uploaded a bugfix to the release repository which should be built and available within a day or two. Look for version 1.10.1. Best, Jim Mayte Suarez-Farinas wrote: > 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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623