[BioC] Error in normalize.AffyBatch.invariantset

[Seth Falcon]

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

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/