R help - Feb 2008 - problem with creation of eSet

Hi,

 

 I am having troubles with creating an eSet and would appreciate any help on
the following problem.

 

I am trying to create an eSet  using the following code 

 

pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);

colnames(pd) <-
c("type","tumor","time","id");

pdN <- list(type
"Cellline/xenograft",tumor="primary,secondary,cellline",time
"0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9")

# Initialize exprSet object

pD <- new("phenoData", pData=pd, varLabels=pdN);

# This is my eSet!!!

metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log),
phenoData=pD)

 

I get the following error:

 

The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead

 

 

Can someone suggest me how to use the new method AnnotatedDataFrame to create
eSet?

 

 

Thanks

 

Manisha

 

 


	[[alternative HTML version deleted]]

Hi Manisha -- this is a bioconductor package, so ask on the
Bioconductor mailing list. The 'exprSet' class is quite old, and has
been replaced by the 'ExpressionSet' class. Update your venison of R
and Bioconductor (http://bioconductor.org/download). Then evaluate the
commands
> library(Biobase)
> openVignette()
and read the first vignette 'Biobase - An introduction to Biobase and
ExpressionSets'.

Hope that helps,

Martin

"Manisha Brahmachary" <mb3058 at c2b2.columbia.edu> writes:
> Hi,
>
>  
>
>  I am having troubles with creating an eSet and would appreciate any help
on
> the following problem.
>
>  
>
> I am trying to create an eSet  using the following code 
>
>  
>
> pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
>
> colnames(pd) <-
c("type","tumor","time","id");
>
> pdN <- list(type >
"Cellline/xenograft",tumor="primary,secondary,cellline",time
> "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9")
>
> # Initialize exprSet object
>
> pD <- new("phenoData", pData=pd, varLabels=pdN);
>
> # This is my eSet!!!
>
> metastasis.eset <- new("exprSet",
exprs=as.matrix(geneExpr.log),
> phenoData=pD)
>
>  
>
> I get the following error:
>
>  
>
> The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
>
>  
>
>  
>
> Can someone suggest me how to use the new method AnnotatedDataFrame to
create
> eSet?
>
>  
>
>  
>
> Thanks
>
>  
>
> Manisha
>
>  
>
>  
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

Hi Manisha,

This is a Bioconductor-specific question. Please repost on the bioc 
listserv:

bioconductor at stat.math.ethz.ch

Best,

Jim



Manisha Brahmachary wrote:
> Hi,
> 
>  
> 
>  I am having troubles with creating an eSet and would appreciate any help
on
> the following problem.
> 
>  
> 
> I am trying to create an eSet  using the following code 
> 
>  
> 
> pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
> 
> colnames(pd) <-
c("type","tumor","time","id");
> 
> pdN <- list(type >
"Cellline/xenograft",tumor="primary,secondary,cellline",time
> "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9")
> 
> # Initialize exprSet object
> 
> pD <- new("phenoData", pData=pd, varLabels=pdN);
> 
> # This is my eSet!!!
> 
> metastasis.eset <- new("exprSet",
exprs=as.matrix(geneExpr.log),
> phenoData=pD)
> 
>  
> 
> I get the following error:
> 
>  
> 
> The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 
>  
> 
>  
> 
> Can someone suggest me how to use the new method AnnotatedDataFrame to
create
> eSet?
> 
>  
> 
>  
> 
> Thanks
> 
>  
> 
> Manisha
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623