[BioC] RE : designing an eSet derived object
Martin Morgan
mtmorgan at fhcrc.org
Mon Nov 22 19:42:12 CET 2010
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]]
>>
>>
>>
>>
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>
>
> -- Computational Biology Fred Hutchinson Cancer Research Center 1100
> Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
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--
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