[Bioc-devel] BUG/TYPO: gcrma::bg.adjust.affinities <- function(..., k=k, ...)

[Zhijin Wu]

Thank you for pointing it out. Since the function is called from a 
higher level one and "k" is always passed from that level it has not 
caused problem for most users. But for someone to directly use this 
function I do need to set the default

Thanks,
Jean
On 9/29/2010 7:58 PM, Henrik Bengtsson wrote:
> [maintainer cc:ed]
>
> Hi,
>
> I looks like there is a cut'n'paste bug in gcrma::bg.adjust.affinities():
>
>> library("gcrma");
>> args(gcrma::bg.adjust.affinities);
> function (pms, ncs, apm, anc, index.affinities, k = k, fast = FALSE,
>      nomm = FALSE)
>
> Note how the default value for argument 'k' is k.  Looks like a
> mistake to me.  Most likely it is not a serious one.
>
>> sessionInfo()
> R version 2.12.0 alpha (2010-09-27 r53048)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] gcrma_2.21.1  affy_1.27.2   Biobase_2.9.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.17.4         Biostrings_2.17.47    IRanges_1.7.34
> [4] preprocessCore_1.11.0 splines_2.12.0        tools_2.12.0
>
> /Henrik


-- 
------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu