[Bioc-devel] accession methods to new ExpressionSet objects

Hi Martino,

Martino Barenco <sejjmba at ucl.ac.uk> writes:
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.
Yes, pData will remain
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
The new ExpressionSet does not require an element se.exprs, so there
is no method defined.
3) But I have found a workaround using assayData 
(Name_of_ExpressionSet)$se.exprs, will this be still valid in the  
near future?
Yes assayData(obj) returns the assay data (list or environment), and $
(or [[) can be used to extract an 'se.exprs' element (if it
exists!). You can check on the names of the assay data elements with
assayDataElementNames.
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.
obj <- assayDataElementReplace(obj, 'se.exprs', <matrix>)

or, with the very latest Biobase

assayDataElement(obj, 'se.exprs') <- <matrix>

do the trick; The awkwardness of the syntax emphasize that these are
departing from the 'usual' ExpressisonSet interface, that somehow the
se.exprs element is different from what an ExpressionSet 'is'. Likely
you should do validObject(obj) after the addition, to make sure that
the object you create is consistent with an ExpressionSet (there may
be row or column name issues with your 'se.exprs' matrix).
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.
Are you thinking of the 'Depends' field? You should probably indicate
the version of Biobase you used when updating your code.
Many thanks and I hope these questions are not too silly, you might  
have guessed that I am a total beginner.
Hope that helps, and feel free to ask further questions if you need
more help.

Martin
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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Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org

[Bioc-devel] accession methods to new ExpressionSet objects

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