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

[Henrik Bengtsson]

I also spotted this one:

> args(gcrma::bg.adjust.fullmodel)
function (pms, mms, ncs = NULL, apm, amm, anc = NULL, index.affinities,
    k = k, rho = 0.7, fast = FALSE)

Thxs,

Henrik

On Thu, Sep 30, 2010 at 6:00 AM, Zhijin Wu <zwu at stat.brown.edu> wrote:
> 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
>
>