[BioC] (no subject)

[Robert Gentleman]

Hi John,
   Have you looked at the vignette in Biobase that explains how to do  
this?
The short answer is that
On Apr 16, 2005, at 7:52 AM, Jiuzhou song wrote:

> Hi,
> I want to creat a exprSet class, it combines expression data and  
> phenotype
> data together. expression data is a matrix with columns representing
> patients and rows respresent genes. The phenoData contains the patient
> level, the column represent level and the rows represent patients. The
> format of the two datasets are shown below:
>
> The gene expression data:
> P01	P02	P03	P04	P05	P06	P07	P08	P09	P10	P11	P12	P13	P14	P15
> 1007_s_at	1336.97	1244.81	1242.41	1514.92	1531.80	1244.61	1030.43	 
> 967.83	866.32
> 1253.16	1218.51	1518.09	1401.07	1281.88	1438.96
> ........
>
> the phenotype data:
>
> Patient Phenotype
> P01	Def
> P02	Def
> P03	Def
> ......
>
> My codes:
>> x<-read.table("exprstry.txt", header=TRUE)
>> y<-read.table("phenotype.txt", header=TRUE)
>> eset<-new('exprSet', exprs=x, phenoData=y)
> Error in validObject(.Object) : Invalid "exprSet" object: 1: Invalid  
> object
> for slot "exprs" in class "exprSet": got class "data.frame", should be  
> or
> extend class "exprMatrix"

read.table returns a data.frame,  you need to turn that into a matrix  
(which is not the same thing)
you might just want to check and see if the data is correct - has row  
names that are meaningful etc.

the second argument needs to be an object of class phenoData, such  
objects do have a data.frame with the sample level covariate  
information but it also has a slot named varLabels where you should put  
a list which describes the variables in your data.frame (and hence  
these are self-documenting data structures).

class?phenoData

will give you information on the class.

Robert

An example copied straight from the vignette:

library(Biobase)


data(geneCov)
data(geneData)
covN <- list(cov1 = "Covariate 1; 2 levels",
              cov2 = "Covariate 2; 2 levels",
              cov3 = "Covariate 3; 3 levels")

pD <- new("phenoData", pData=geneCov, varLabels=covN)
eSet <- new("exprSet", exprs=geneData, phenoData=pD)





> Invalid "exprSet" object: 2: Invalid object for slot "phenoData" in  
> class
> "exprSet": got class "data.frame", should be or extend class  
> "phenoData"
>
> Why it doesn't work.
> Thanks.
>
> Yours
>
> John
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
+----------------------------------------------------------------------- 
----------------+
| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
       |
| Fred Hutchinson Cancer Research Center                                 
          |
| email: rgentlem at fhcrc.org                                              
                          |
+----------------------------------------------------------------------- 
----------------+


+----------------------------------------------------------------------- 
----------------+
| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
       |
| Fred Hutchinson Cancer Research Center                                 
          |
| email: rgentlem at fhcrc.org                                              
                          |
+----------------------------------------------------------------------- 
----------------+