Hi,

I am in the process of updating the package I am maintaining (rHVDM)  
in the view of the upcoming deprecation of exprSet objects R2.5/ 
BiobaseX.Y and I have a few questions about accession methods of the  
new ExpressionSet objects. In particular:

1) Will the pData method be still valid in the near future? I am  
asking because it is semantically identical to the old one.
2) The se.exprs method does not work on R2.4.0/Biobase 1.12.2,  
actually, it is more a remark than a question
3) But I have found a workaround using assayData 
(Name_of_ExpressionSet)$se.exprs, will this be still valid in the  
near future?
4) I also need to be able to modify the se.exprs matrix and the above  
command does not allow that, the only way this can be done is by  
reallocating a whole new object.
5) This update completely passed under my (admitedly poor) radar: in  
which R/Biobase were these changes first introduced so that I can  
update the "DESCRIPTION" file as well. I am interested in backward-  
as much as forward- compatibility.

Many thanks and I hope these questions are not too silly, you might  
have guessed that I am a total beginner.

Martino



Here is the relevant listing, I am converting an exprSet object  
(fiveGyMAS5) into a new ExpressionSet object (fiveGyMAS5), note that  
it has two data slots (exprs and se.exprs):

 > class(fiveGyMAS5)
[1] "exprSet"
attr(,"package")
[1] "Biobase"
 > fiveGyMAS5_ES<-as(fiveGyMAS5,"ExpressionSet")
 > fiveGyMAS5_ES
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 21 samples
   element names: exprs, se.exprs
phenoData
   sampleNames: cARP3-6hrs.CEL, cARP3-2hrs.CEL, ..., cARP3-10hrs.CEL  
(21 total)
   varLabels and varMetadata:
     replicate: NULL
     time: NULL
     experiment: NULL
featureData
   featureNames: 1007_s_at, 1053_at, ..., AFFX-r2-P1-cre-5_at (22283  
total)
   varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "hgu133a"
 > pData(fiveGyMAS5_ES)
                 replicate time experiment
cARP3-6hrs.CEL          3    6        5Gy
cARP3-2hrs.CEL          3    2        5Gy
cARP3-0hrs.CEL          3    0        5Gy
cARP2-0hrs.CEL          2    0        5Gy
cARP2-12hrs.CEL         2   12        5Gy
cARP1-6hrs.CEL          1    6        5Gy
cARP1-12hrs.CEL         1   12        5Gy
cARP1-2hrs.CEL          1    2        5Gy
cARP3-8hrs.CEL          3    8        5Gy
cARP2-8hrs.CEL          2    8        5Gy
cARP3-12hrs.CEL         3   12        5Gy
cARP1-0hrs.CEL          1    0        5Gy
cARP2-4hrs.CEL          2    4        5Gy
cARP1-8hrs.CEL          1    8        5Gy
cARP2-10hrs.CEL         2   10        5Gy
cARP2-2hrs.CEL          2    2        5Gy
cARP1-4hrs.CEL          1    4        5Gy
cARP2-6hrs.CEL          2    6        5Gy
cARP3-4hrs.CEL          3    4        5Gy
cARP1-10hrs.CEL         1   10        5Gy
cARP3-10hrs.CEL         3   10        5Gy
 > exprs(fiveGyMAS5_ES)[1,]
cARP3-6hrs.CEL  cARP3-2hrs.CEL  cARP3-0hrs.CEL  cARP2-0hrs.CEL  
cARP2-12hrs.CEL
        142.3257         78.6030         78.2122          
82.0896        162.3600
cARP1-6hrs.CEL cARP1-12hrs.CEL  cARP1-2hrs.CEL  cARP3-8hrs.CEL   
cARP2-8hrs.CEL
        152.0475        141.0750         97.6976         
176.5356        222.5884
cARP3-12hrs.CEL  cARP1-0hrs.CEL  cARP2-4hrs.CEL  cARP1-8hrs.CEL  
cARP2-10hrs.CEL
        156.5543         99.3000        125.4226         
130.5018        175.9454
cARP2-2hrs.CEL  cARP1-4hrs.CEL  cARP2-6hrs.CEL  cARP3-4hrs.CEL  
cARP1-10hrs.CEL
         85.4280        106.2817        170.4510          
90.2580        157.8746
cARP3-10hrs.CEL
        185.9463
 > se.exprs(fiveGyMAS5_ES)[1,]
Error in function (classes, fdef, mtable)  :
	unable to find an inherited method for function "se.exprs", for  
signature "ExpressionSet"
 > assayData(fiveGyMAS5_ES)$se.exprs[1,]
cARP3-6hrs.CEL  cARP3-2hrs.CEL  cARP3-0hrs.CEL  cARP2-0hrs.CEL  
cARP2-12hrs.CEL
        21.20778        15.79627        14.20352         
12.50463        20.83215
cARP1-6hrs.CEL cARP1-12hrs.CEL  cARP1-2hrs.CEL  cARP3-8hrs.CEL   
cARP2-8hrs.CEL
        17.21553        16.22317        13.97164         
31.00531        38.83279
cARP3-12hrs.CEL  cARP1-0hrs.CEL  cARP2-4hrs.CEL  cARP1-8hrs.CEL  
cARP2-10hrs.CEL
        21.60900        13.49323        18.31659         
14.55734        22.28536
cARP2-2hrs.CEL  cARP1-4hrs.CEL  cARP2-6hrs.CEL  cARP3-4hrs.CEL  
cARP1-10hrs.CEL
        14.94011        14.53037        24.42759         
17.59149        19.52623
cARP3-10hrs.CEL
        30.85853


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