[BioC] limma2biomaRt error

[James W. MacDonald]

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)
> 
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-- 
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