[BioC] bug in Biobase:split

A.J. Rossini rossini@u.washington.edu
16 Jul 2002 13:46:14 -0700


Something to be careful of -- I've worked around it, but don't have
time for the real patch.

The problem:

split(exprSet,factor) fails, while 
split(exprSet,as.numeric(factor)) works:

The example:

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[Previously saved workspace restored]

> options(STERM='iESS', editor='emacsclient')
Warning message: 
using .GlobalEnv instead of package:annotate 
> library(Biobase)
Loading required package: methods 
Expanding the signature to include omitted arguments 
in definition: j = "missing" 

Attaching package `Biobase':


	The following object(s) are masked from package:base :

	 split 

> geary
Expression Set (exprSet) with 
	4132 genes
	8 samples
		 phenoData object with 2 variables and 8 cases
	 varLabels
		animal: Animal
		type: Specimen Type
> split(geary,geary$animal) 
$"1"
Expression Set (exprSet) with 
	4132 genes
	2 samples
		 phenoData object with 2 variables and 2 cases
	 varLabels
		animal: Animal
		type: Specimen Type

$"2"
Expression Set (exprSet) with 
	4132 genes
	2 samples
		 phenoData object with 2 variables and 2 cases
	 varLabels
		animal: Animal
		type: Specimen Type

$"3"
Expression Set (exprSet) with 
	4132 genes
	2 samples
		 phenoData object with 2 variables and 2 cases
	 varLabels
		animal: Animal
		type: Specimen Type

$"4"
Expression Set (exprSet) with 
	4132 genes
	2 samples
		 phenoData object with 2 variables and 2 cases
	 varLabels
		animal: Animal
		type: Specimen Type

> geary$animal
[1] 1 1 2 2 3 3 4 4
> split(geary,geary$type)
$Gunk
Expression Set (exprSet) with 
	2066 genes
	8 samples
		 phenoData object with 2 variables and 8 cases
	 varLabels
		animal: Animal
		type: Specimen Type

$Other
Expression Set (exprSet) with 
	2066 genes
	8 samples
		 phenoData object with 2 variables and 8 cases
	 varLabels
		animal: Animal
		type: Specimen Type

> geary$type
[1] Gunk  Other Gunk  Other Gunk  Other Gunk  Other 
Levels:   Gunk  Other
> split(geary,as.numeric(geary$type))
$"1"
Expression Set (exprSet) with 
	4132 genes
	4 samples
		 phenoData object with 2 variables and 4 cases
	 varLabels
		animal: Animal
		type: Specimen Type

$"2"
Expression Set (exprSet) with 
	4132 genes
	4 samples
		 phenoData object with 2 variables and 4 cases
	 varLabels
		animal: Animal
		type: Specimen Type

> q()




-- 
A.J. Rossini				Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics		rossini@u.washington.edu	
FHCRC/SCHARP/HIV Vaccine Trials Net	rossini@scharp.org
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