[BioC] Error in normalize.AffyBatch.invariantset

[Markus Schmidberger]

Hi,

here the missing information:

 > sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"    

other attached packages:
    affy   affyio  Biobase
"1.14.2"  "1.4.1" "1.14.1"

Best,
Markus


Seth Falcon schrieb:
> Hi Markus,
>
> Markus Schmidberger <schmidb at ibe.med.uni-muenchen.de> writes:
>   
>> Hello,
>>
>> I found a simple error in the "normalize.AffyBatch.invariantset" 
>> function. On line 72, there is a "nunlist". I think this should be a unlist!
>>
>>  else if (type == "together") {
>>         pms <- nunlist(indexProbes(abatch, "both"))
>>         do.normalize.Affybatch.invariantset(abatch, pms, prd.td,
>>             baseline.type)
>>     }
>>     
>
> Thanks for the report.  This was fixed in the development version of
> the affy package on 10 May.  The fix applied was:
>
> --- a/affy/R/normalize.invariantset.R
> +++ b/affy/R/normalize.invariantset.R
> @@ -78,7 +78,7 @@ normalize.AffyBatch.invariantset <- function(abatch, prd.td=c(
>      pms <- unlist(mmindex(abatch))
>      do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type)
>    } else if (type == "together"){
> -    pms <- nunlist(indexProbes(abatch,"both"))
> +    pms <- unlist(indexProbes(abatch,"both"))
>      do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type)
>    } else if (type == "separate"){
>      pms <- unlist(pmindex(abatch))
>
> I hope you will continue to send such reports to the list, but when
> you do, please remember to include package name, version number, R
> version, etc.
>
> Best,
>
> + seth
>
>   


-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599