[BioC] RE : designing an eSet derived object

[Martin Morgan]

On 11/24/2010 05:47 AM, Wolfgang RAFFELSBERGER wrote:
> Dear Martin,
> 
> thank's again - I've got things working as you explained.
> 
> Just to make sure I completely understood: Now everything is
> streamlined for the storage of the multiple ExperssionSets for the
> various methods employed (the 1st slot in my GxSet). The next step is
> then to review how I'm storing the "derived" data (eg averages,
> SEM,...   for each of the methods from above).  Here I've tried a few
> things, but as far as I understand, there is no already existing
> class close enough to my case (ideally a "SimpleListList" = list of
> SimpleLists). So I made a new class containing multiple SimpleList
> objects (code below) :
> 
> setClass("GxAvData",representation(avSI="SimpleList",expressed="SimpleList",SEM="SimpleList",
>  
> FC="SimpleList",FiltFin="SimpleList",FiltSI="SimpleList",FiltOther="SimpleList"))
> 
> 
> I've also tried to use the SimpleMatrixList object since all my
> (final) data are nothing but matrixes, but I didn't get this working.
> Does this matter much ? Or should I rather define a general
> "SimpleListList" (list of SimpleLists) first, to decline my specific
> class ("GxAvData") of this ?

It seems like your class has a well-defined number of 'SimpleList'
slots, so your setClass above seems appropriate.

If I

setClass("SimpleMatrixList", contains="SimpleList",
         prototype=prototype(elementType="matrix"))
SimpleMatrixList <-
    function(...) new("SimpleMatrixList", listData=list(...))

things seem to work?

> mlst <- SimpleMatrixList(a=matrix(0, 5, 5), b=matrix(1, 5, 5))
> mlst[["b"]]
     [,1] [,2] [,3] [,4] [,5]
[1,]    1    1    1    1    1
[2,]    1    1    1    1    1
[3,]    1    1    1    1    1
[4,]    1    1    1    1    1
[5,]    1    1    1    1    1
> mlst <- SimpleMatrixList(c=data.frame())
Error in validObject(.Object) :
  invalid class "SimpleMatrixList" object: the 'listData' slot must be a
list containing matrix objects

Martin

> 
> 
> Thanks for all your helpful comments,
> 
> Wolfgang
> 
> PS: Hope you had a good travel back to the US.
> 
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et
> Génomique Intégratives IGBMC, 1 rue Laurent Fries,  67404 Illkirch
> Strasbourg,  France Tel (+33) 388 65 3300         Fax (+33) 388 65
> 3276 wolfgang.raffelsberger (at ) igbmc.fr
> 
> ________________________________________ De :
> bioconductor-bounces at stat.math.ethz.ch
> [bioconductor-bounces at stat.math.ethz.ch] de la part de Martin Morgan
> [mtmorgan at fhcrc.org] Date d'envoi : lundi 22 novembre 2010 19:42 À :
> Wolfgang RAFFELSBERGER Cc : bioconductor at stat.math.ethz.ch Objet :
> Re: [BioC] RE :  designing an eSet derived object
> 
> Hi Wolfgang --
> 
> On 11/22/2010 03:44 AM, Wolfgang RAFFELSBERGER wrote:
>> Dear Martin,
>> 
>> thank you very much for your helpful input. I'm sorry I have to
>> bug you again.
> 
>> I was about there, but at the recent Bioconductor Developer Meeting
>> I got another intersting suggestion, which I haven't succeded 
>> implementing.
> 
>> Briefly, (if I understood right) the idea was rather to make a 
>> modified SimpleList class where I could check that each elment is
>> an expression set  (instead of using the SimpleList class as is).
>> From there one might even go one step further and check if all
>> dimensions are identical, too ...
>> 
>> For the making the modified SimpleList I returned to the help 
>> provided in the Bioconductor pdf "Biobase development and the new 
>> eSet". But it seems I'm not getting the inizialization right.
> 
>> My 'problem' is, that I don't want to fix in advance how many 
>> ExperssionSets will be put in the list (SimpleList), neither what 
>> their names will be.  This way I hope the object will be 
>> sufficienltly general to hold results from normalization-methods
>> that might become available in the future. Now, this is now quite 
>> different to the example provided in  "Biobase development and the 
>> new eSet".
>> 
>> To link to my previous post: This (modified) SimpleList will then
>> be used as a slot (allowing to store data normalized by multiple 
>> methods) of another new class (the "GxSet"), plus in other slots
>> for data-derived values (averages, etc) and more
>> documentation/notes)...
>> 
>> Thank's in advance fro any hints, Wolfgang
> 
>> 
>> 
>>> 
>>> require(Biobase); require(IRanges); require(affy) # the toy data 
>>> eset1 <- new("ExpressionSet", exprs=matrix(1,10,4)) pData(eset1)
>>> <- data.frame("class"=c(1,2,2,2))
>>> 
>>> eset2 <- new("ExpressionSet", exprs=matrix(3,10,4)) pData(eset2)
>>> <- data.frame("class"=c(1,2,2,2))
>>> 
>>> # making the modified class 
>>> setClass("GxSimpleList",contains="SimpleList")
> 
> I think the idea is
> 
> setClass("SimpleExpressionSetList", contains="SimpleList", 
> prototype=prototype(elementType="ExpressionSet"))
> 
> and then you're done...
> 
>> listData1 <- list(A=new("ExpressionSet"), B=new("ExpressionSet")) 
>> listData2 <- list(A=new("ExpressionSet"), B=matrix()) 
>> new("SimpleExpressionSetList", listData=listData1)
> SimpleExpressionSetList of length 2 names(2): A B
>> new("SimpleExpressionSetList", listData=listData2)
> Error in validObject(.Object) : invalid class
> "SimpleExpressionSetList" object: the 'listData' slot must be a list
> containing ExpressionSet objects
>> 
> 
>> [1] "GxSimpleList"
>>> getClass("GxSimpleList")
>> Class "GxSimpleList" [in ".GlobalEnv"]
>> 
>> Slots:
>> 
>> Name:         listData elementMetadata     elementType metadata
>> Class:            list             ANY       character list
>> 
>> Extends: Class "SimpleList", directly Class "Sequence", by class 
>> "SimpleList", distance 2 Class "Annotated", by class "SimpleList", 
>> distance 3
>>> 
>>> # for the "initialize" I didn't understand how to formulate it
>>> in my case (as I don't know how many elements, neither their
>>> names) setMethod("initialize","GxSimpleList",
>>> function(.object,...) listData =
>>> listDataNew(lapply(list(.object,...) == "ExpressionSet") ))
>> Error in conformMethod(signature, mnames, fnames, f, fdef, 
>> definition) : in method for ‘initialize’ with signature 
>> ‘.Object="GxSimpleList"’: formal arguments (.Object =
>> "GxSimpleList", ... = "GxSimpleList") omitted in the method
>> definition cannot be in the signature
>>> 
>>> setMethod("initialize","GxSimpleList", function(.object,...) 
>>> {.object <- callNextMethod(.object,...)})
>> Error in conformMethod(signature, mnames, fnames, f, fdef, 
>> definition) : in method for ‘initialize’ with signature 
>> ‘.Object="GxSimpleList"’: formal arguments (.Object =
>> "GxSimpleList", ... = "GxSimpleList") omitted in the method
>> definition cannot be in the signature
>>> 
>>> # I guess the check for experssionSets should go into validity 
>>> setValidity("GxSimpleList", function(object) {   # experimetal
>> +    if(sum(!(unlist(lapply(object,function(x) class(x))) %in% 
>> "ExpressionSet")) >0) "A 'GxSimpleList' object should contain 
>> elements of class 'ExpressionSet' only !" +    #same as ?# 
>> assayDataValidMembers(class(object), 
>> rep("ExpressionSet",length(object))) +    }) Class "GxSimpleList"
>> [in ".GlobalEnv"]
>> 
>> Slots:
>> 
>> Name:         listData elementMetadata     elementType metadata
>> Class:            list             ANY       character list
>> 
>> Extends: Class "SimpleList", directly Class "Sequence", by class 
>> "SimpleList", distance 2 Class "Annotated", by class "SimpleList", 
>> distance 3
>>> 
>>> # what happens .. lst1 = SimpleList(a=eset1, b=eset2)   # OK
>>> 
>>> lst2 = new("GxSimpleList",a=eset1, b=eset2)  # error (due to 
>>> missing "initialize" ?)
>> Error in initialize(value, ...) : invalid names for slots of class 
>> "GxSimpleList": a, b
>>> lst3 = GxSimpleList(a=eset1, b=eset2)        # error (due to 
>>> missing "initialize" ?)
>> Error: could not find function "GxSimpleList"
>>> 
>>> # for completeness ... sessionInfo()
>> R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 
>> (32-bit)
>> 
>> locale: [1] LC_COLLATE=French_France.1252 
>> LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 
>> LC_NUMERIC=C [5] LC_TIME=French_France.1252
>> 
>> attached base packages: [1] grDevices datasets  splines   graphics 
>> stats     tcltk     utils     methods   base
>> 
>> other attached packages: [1] affy_1.28.0     IRanges_1.8.0 
>> Biobase_2.10.0  svSocket_0.9-50 TinnR_1.0.3     R2HTML_2.2 
>> Hmisc_3.8-3     survival_2.35-8
>> 
>> loaded via a namespace (and not attached): [1] affyio_1.18.0 
>> cluster_1.13.1        grid_2.12.0           lattice_0.19-13 
>> preprocessCore_1.12.0 svMisc_0.9-60 [7] tools_2.12.0
>>> 
>> 
>> 
>> 
>> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>> . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et 
>> Génomique Intégratives IGBMC, 1 rue Laurent Fries,  67404 Illkirch 
>> Strasbourg,  France Tel (+33) 388 65 3300         Fax (+33) 388 65 
>> 3276 wolfgang.raffelsberger (at ) igbmc.fr
>> 
>> ________________________________________ De : Martin Morgan 
>> [mtmorgan at fhcrc.org] Date d'envoi : vendredi 5 novembre 2010 18:33
>> À : Wolfgang RAFFELSBERGER Cc : bioconductor at stat.math.ethz.ch
>> Objet : Re: [BioC] designing an eSet derived object
>> 
>> On 11/05/2010 05:02 AM, Wolfgang RAFFELSBERGER wrote:
>>> Dear list,
>>> 
>> 
>>> basically I'm trying to design an object to contain the
>>> following microarray-data 1) "gxIndData": microarray-data
>>> normalized in parallel by (an array-dependent) number of n
>>> methods plus the corresponding expression-calls (again, <= n
>>> methods), 2) "gxAvData": derived values (replicate-averages,
>>> SEMs, etc), 3) gene/spot annotation, 4) sample-description, 5)
>>> various supl informations (parameters, notes, versions, etc)
>>> 
>>> In overall, this is a somehow modified/extended concept to the 
>>> Biobase eSet and I'm trying to figure out if there is a way to
>>> use the Biobase eSet. This way I hope to maintain a decent level
>>> of compatibility with other Bioconductor methods and allow 
>>> code-reuse.
>>> 
>>> Now I'd like to store  the various sections of 1) and 2) as 
>>> separate lists with n matrixes of values to keep things
>>> organized.
>>> 
>>> According to the Vignette "Biobase development and the new eSet" 
>>> section 5 ("Extending eSet"), I defined new a new class 'eSet'. 
>>> But as soon as I integrate something different than matrixes at
>>> the level of 'AssayData', I get an error-message (see code below)
>>> - no matter if these are simply lists or custom-objects. I
>>> suppose this means that I would have to store all matrixes (up to
>>> 10*6methods =60 matrixes) without further organization at the
>>> level of 'AssayData'.
>> 
>> eSet requires that all AssayData elements are two-dimensional with 
>> identical dimensions, so a list-of-matrices would not work.
>> 
>>> However, I'd like to keep at least one (in my case better 2) 
>>> levels of additional arborescence to keep the data organized.
>>> 
>>> So, finally I would like to integrate two new classes for 1) and 
>>> 2) at the level of the assayData slot of my modified/new eSet.
>>> 
>>> Does this mean this is not possible and that I cannot use the 
>>> 'eSet' for my purposes ? Do I have to create a novel class
>>> somehow equivalent but finally incompatible to the 'eSet' ?
>>> 
>>> Any suggestions/hints ?
>> 
>> One possiblity, if this is for your own use and not as the 
>> foundation for a package, is to use NChannelSet, where each method
>> is a 'channel'.
>> 
>> Another possibility is to create a class that extends eSet with a 
>> slot containing, e.g., an AnnotatedDataFrame with columns
>> describing the AssayData, and a method to query the slot / select
>> the appropriate assayData elements
>> 
>> And perhaps what you really have is more a list of (of lists of) 
>> ExpressionSets, each element of the list with additional
>> information. An approach here would use the IRanges 'SimpleList'
>> infrastructure, e.g.,
>> 
>>> lst = SimpleList(a=new("ExpressionSet"), b=new("ExpressionSet")) 
>>> elementMetadata(lst) = DataFrame(method=c("A", "B")) 
>>> lst[elementMetadata(lst)$method == "A"]
>> SimpleList of length 1 names(1): a
>>> lst[elementMetadata(lst)$method == "A"][[1]]
>> ExpressionSet (storageMode: lockedEnvironment) assayData: 0
>> features, 0 samples element names: exprs protocolData: none
>> phenoData: none featureData: none experimentData: use
>> 'experimentData(object)' Annotation:
>> 
>> Martin
>> 
>>> 
>>> Thank’s in advance, wolfgang
>>> 
>>> ##
>>> 
>>> require(Biobase) setClass("gxSet", contains = "eSet") 
>>> setMethod("initialize", "gxSet", function(.Object, 
>>> A=new("list"),B=new("list"),...) { callNextMethod(.Object,
>>> A=A,B=B, ...) }) new("gxSet") ## produces : Error in function
>>> (storage.mode = c("lockedEnvironment", "environment",  :
>>> 'AssayData' elements with invalid dimensions: 'A' 'B'
>>> 
>>> 
>>> ## ideally I'd like to use 
>>> setClass("gxIndData",representation(SIdata="list",SIcall="list"))
>>>
>>> 
setClass("gxAvData",representation(avSI="list",expressed="list",SEM="list",
>>> conCall="list", 
>>> FC="list",FiltFin="list",FiltSI="list",FiltOther="list")) 
>>> setClass("gxSet", contains = "eSet")
>>> 
>>> setMethod("initialize","gxSet", function(.Object, 
>>> assayData=assayDataNew(IndData=IndData,AvData=AvData), 
>>> IndData=new("gxIndData"), AvData=new("gxAvData"),...) { 
>>> if(!missing(assayData) && any(!missing(IndData),
>>> !missing(AvData))) { warning("using 'assayData'; ignoring
>>> 'IndData', 'AvData'") } callNextMethod(.Object, assayData =
>>> assayData, ...) })
>>> 
>>> new("gxSet") ## produces : Error in assayDataNew(IndData =
>>> IndData, AvData = AvData) : 'AssayData' elements with invalid
>>> dimensions: 'AvData' 'IndData'
>>> 
>>> 
>>> ## the alternative : an eSet 'like' but independent and 
>>> incompatible object .. 
>>> setClass("gxSet",representation(IndData="gxIndData",AvData="gxAvData",phenoData="AnnotatedDataFrame",featureData="AnnotatedDataFrame",
>>>
>>>
>
>>> 
experimentData="MIAME",annotation="character",protocolData="AnnotatedDataFrame",notes="list"))
>>> 
>>> 
>>> 
>>> ## for completeness: sessionInfo() R version 2.12.0 (2010-10-15) 
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>> 
>>> locale: [1] LC_COLLATE=French_France.1252 
>>> LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252
>>> [4] LC_NUMERIC=C                   LC_TIME=French_France.1252
>>> 
>>> attached base packages: [1] grDevices datasets  splines
>>> graphics stats     tcltk     utils     methods   base
>>> 
>>> other attached packages: [1] affy_1.28.0     Biobase_2.10.0 
>>> svSocket_0.9-50 TinnR_1.0.3     R2HTML_2.2      Hmisc_3.8-3 
>>> survival_2.35-8
>>> 
>>> loaded via a namespace (and not attached): [1] affyio_1.18.0 
>>> cluster_1.13.1        grid_2.12.0           lattice_0.19-13 
>>> preprocessCore_1.12.0 [6] svMisc_0.9-60         tools_2.12.0
>>> 
>>> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>>> . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique
>>> et Génomique Intégratives IGBMC, 1 rue Laurent Fries,  67404
>>> Illkirch Strasbourg,  France Tel (+33) 388 65 3300         Fax
>>> (+33) 388 65 3276 wolfgang.raffelsberger @ igbmc.fr
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________ Bioconductor 
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>>
>>
>>
>>> 
-- Computational Biology Fred Hutchinson Cancer Research Center 1100
>> Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>> 
>> Location: M1-B861 Telephone: 206 667-2793
> 
> 
> -- Computational Biology Fred Hutchinson Cancer Research Center 1100
> Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
> Location: M1-B861 Telephone: 206 667-2793
> 
> _______________________________________________ Bioconductor mailing
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-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793