[BioC] Does old workspace work?
Martin Morgan
mtmorgan at fhcrc.org
Thu Oct 30 23:42:44 CET 2008
Loren Engrav wrote:
> Thank you
>
> str(obj) returned
> @ se.exprs : num [0 , 0]
> so I guess there were none
>
> I find on the web se.exprs is/was standard error estimates
>
> The old object came in Jan Feb Mar of 2007 as below
>
> AA_ReadAffy <- ReadAffy() to read 60 Affy .cel files
> ABeset_gcrma <- gcrma (AA_ReadAffy) to gcrma it
>
> After the above I went on and did library (maanova) stuff
>
> Does it matter if the old ABeset_gcrma object had no std error estimates?
Few downstream steps made use of the standard errors, and many upstream
methods (including gcrma) didn't / couldn't produce standard errors.
Martin
>> From: Martin Morgan <mtmorgan at fhcrc.org>
>> Date: Thu, 30 Oct 2008 13:33:55 -0700
>> To: Loren Engrav <engrav at u.washington.edu>
>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] Does old workspace work?
>>
>> Hi Loren --
>>
>> Loren Engrav <engrav at u.washington.edu> writes:
>>
>>> With the show(obj) function and the write.table function, I can see the
>>> stuff in the old objects so that may solve the immediate problem
>>>
>>> But changing exprSet to ExpressionSet is attractive
>>> And I see it has been discussed before (see below)
>>>
>>> ===========================
>>> [BioC] Error loading, on Bioconductor 1.8, exprSet generated with
>>> bioconductor 1.7
>>> Martin Morgan mtmorgan at fhcrc.org
>>> Thu Jun 8 18:11:14 CEST 2006
>>>
>>> Previous message: [BioC] Error loading, on Bioconductor 1.8,
>>> exprSet generated with bioconductor 1.7
>>> Next message: [BioC] [SPAM] Re: Error loading, on Bioconductor 1.8,
>>> exprSet generated with bioconductor 1.7
>>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>>
>>> Hi Raf,
>>>
>>> Thanks for the clarification. It sounds like you've found a good
>>> solution.
>>>
>>> The long-term intention is to move away from exprSet as the basic
>>> building block, and toward a similar 'ExpressionSet' class. With this
>>> in mind, you could also have done (with the current version of
>>> Biobase)
>>>
>>>> obj <- as(tr7.rma, "ExpressionSet")
>>> to obtain an ExpressionSet from your (broken) exprSet. An
>>> ExpressionSet has methods like exprs(), phenoData(), and pData() that
>>> work as exprSet methods, so for many purposes having an ExpressionSet
>>> is a great replacement for exprSet.
>>>
>>> It's important to be able to return to previous versions of objects,
>>> and make them 'current'. To that end, the development version of
>>> Biobase introduces ways of 'versioning' objects (so that it's easy to
>>> figure out when the object was created) and an 'updateObject' method
>>> to bring an object up to date. So in the next release of Biobase
>>> (available to those already using the 'development' branch of R)
>>> you'll be able to
>>>
>>>> obj <- updateObject(tr76.rma)
>>> and stand a reasonable chance of getting an object that satisfies the
>>> current definition of exprSet.
>>> =============================================
>>>
>>> So I try
>>>> ABeset_gcrmaExpressionSet <- as (ABeset_gcrma, "ExpressionSet")
>>> And get
>>>
>>> Loading required package: Biobase
>>> Loading required package: tools
>>>
>>> Welcome to Bioconductor
>>>
>>> Vignettes contain introductory material. To view, type
>>> 'openVignette()'. To cite Bioconductor, see
>>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>
>>> Warning message:
>>> In asMethod(object) :
>>> missing or mis-shaped 'se.exprs' in original object; creating
>>> ExpressionSet without se.exprs
>> At this point I think ABeset_gcrmaExpressionSet is fine; this is a
>> 'warning' message, not an error. The exprSet instance was 'supposed'
>> to contain an se.exprs matrix, but my guess is that ABeset_gcrma did
>> not (many exprSet instances did not). You might have luck with
>>
>>> str(ABeset_gcrma)
>> you might see something like (it's a little hard to recreate this on
>> 2.8.0)
>>
>> Formal class 'exprSet' [package "Biobase"] with 8 slots
>> ..@ exprs : num [1:500, 1:26] 192.7 97.1 45.8
>> .. ..- attr(*, "dimnames")=List of 2
>> .. .. ..$ : chr [1:500] "AFFX-MurIL2_at" "AFFX-MurIL10_at"
>> .. .. ..$ : chr [1:26] "A" "B" "C" "D" ...
>> ..@ se.exprs : num [1:500, 1:26] 2.85 3.24 3.05
>> .. ..- attr(*, "dimnames")=List of 2
>> .. .. ..$ : chr [1:500] "AFFX-MurIL2_at" "AFFX-MurIL10_at"
>> .. .. ..$ : chr [1:26] "A" "B" "C" "D" ...
>>
>> etc if se.exprs has dimensions 0 (instead of 'chr [1:500]' and 'chr
>> [1:26]' in the example above) then the se.exprs was missing or empty
>> and hence its loss not important. If it's not missing, then you can
>> decide how aggressively you want to rehabilitate your data. Likely
>> you'll be able to retrieve the se.exprs with
>>
>>> se <- slot(ABeset_gcrma, "se.exprs")
>> manipulate it to have the same dimenions and dimnames as your
>> ExpressionSet has, and add it, e.g.,
>>
>>> assayData(ABeset_gcrmaExpressionSet)[["se.exprs"]] <- se
>> I think normally you'll not have to go through these steps though, the
>> se.exprs of exprSet will have had no data in it.
>>
>>> Then I try
>>>> ABeset_gcrmaUPDATE <- updateObject(ABeset_gcrma)
>>> And get
>>> Error in updateObjectFromSlots(object, ..., verbose = verbose) :
>>> could not updateObject to class 'phenoData'
>>> consider defining an 'updateObject' method for class 'phenoData'
>> updateObject is meant to update 'within a class', e.g., from an old
>> version of ExpressionSet to a new version of ExpressionSet. Use 'as'
>> and you are probably ok.
>>
>> There may be issues, especially with very old exprSets, so let me know
>> if you have problems.
>>
>> Martin
>>
>>
>>> All with
>>>> sessionInfo()
>>> R version 2.8.0 Patched (2008-10-26 r46783)
>>> i386-apple-darwin9.5.0
>>>
>>> locale:
>>> C
>>>
>>> attached base packages:
>>> [1] tools stats graphics grDevices utils datasets methods
>>> base
>>>
>>> other attached packages:
>>> [1] Biobase_2.2.0
>>>
>>>> .Machine$sizeof.pointer
>>> [1] 8
>>>
>>> Now since I can "see" the data with show and write.table I should probably
>>> quit, but for the fun of it, are either of these messages a "quick fix" for
>>> a novice?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> From: Robert Gentleman <rgentlem at fhcrc.org>
>>>> Date: Tue, 28 Oct 2008 11:57:36 -0700
>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>> Subject: Re: [BioC] Does old workspace work?
>>>>
>>>> -----BEGIN PGP SIGNED MESSAGE-----
>>>> Hash: SHA1
>>>>
>>>> Re the quality of the link: You need to ask the owner, not this list
>>>>
>>>> and the answer to your second question is that it depends on what you
>>>> want to catch up on. Ideally packages should have up to date vignettes,
>>>> and they are your main starting point. Contact maintainers if the
>>>> vignettes are incomplete or out of date.
>>>>
>>>> best wishes
>>>> Robert
>>>>
>>>> Loren Engrav wrote:
>>>>> Ok, I can deal with change
>>>>>
>>>>> One more question, to learn about and deal with the deprecated stuff
>>>>>
>>>>> Is the file at the url below current, or out of date?
>>>>>
>>>>>
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#Bio>>>>
> C
>>>>> primer
>>>>>
>>>>> If it is out of date, is there a better url to catch up fast?
>>>>>
>>>>>> From: Robert Gentleman <rgentlem at fhcrc.org>
>>>>>> Date: Tue, 28 Oct 2008 09:56:31 -0700
>>>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>>>> Subject: Re: [BioC] Does old workspace work?
>>>>>>
>>>>> Loren Engrav wrote:
>>>>>>>> Ok, I will get my stuff modern
>>>>>>>> One more question
>>>>>>>> Those old saved workspaces and histories might be 32bit from before I
>>>>>>>> went
>>>>>>>> to 64bit
>>>>>>>> If they are 32bit workspaces will they work in 64bit (save for the
>>>>>>>> deprecated stuff)
>>>>> Currently that is the case. But I am not sure how long it will remain
>>>>> so, as it means that R cannot be truly 64bit, so likely in the next year
>>>>> or so some change will be needed. Of course, one will always be able to
>>>>> read 32 bit workspaces in 64bits, but the converse will not likely hold
>>>>> for very much longer
>>>>>
>>>>> Robert
>>>>>
>>>>>
>>>>>>>>> From: Robert Gentleman <rgentlem at fhcrc.org>
>>>>>>>>> Date: Mon, 27 Oct 2008 22:31:21 -0700
>>>>>>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>>>>>>> Subject: Re: [BioC] Does old workspace work?
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> Loren Engrav wrote:
>>>>>>>>>>> sessionInfo()
>>>>>>>>>> R version 2.8.0 Patched (2008-10-26 r46783)
>>>>>>>>>> i386-apple-darwin9.5.0
>>>>>>>>>>
>>>>>>>>>> locale:
>>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>>>>
>>>>>>>>>> attached base packages:
>>>>>>>>>> [1] splines tools stats graphics grDevices utils
>>>>>>>>>> datasets
>>>>>>>>>> methods base
>>>>>>>>>>
>>>>>>>>>> other attached packages:
>>>>>>>>>> [1] simpleaffy_2.18.0 genefilter_1.22.0 survival_2.34-1
>>>>>>>>>> affyio_1.10.0
>>>>>>>>>> porcinecdf_2.3.0 gcrma_2.14.0 matchprobes_1.14.0 affy_1.20.0
>>>>>>>>>> Biobase_2.2.0
>>>>>>>>>>
>>>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>>>> [1] AnnotationDbi_1.4.0 DBI_0.2-4 RSQLite_0.7-1
>>>>>>>>>> annotate_1.20.0 preprocessCore_1.4.0
>>>>>>>>>>
>>>>>>>>>> ==============
>>>>>>>>>> A year or so ago I ran 64bit R on Mac PPC and saved various workspaces
>>>>>>>>>>
>>>>>>>>>> Now am running 64bit R on Intel 2x3.2 QuadCore and MacOS 10.5.5
>>>>>>>>>>
>>>>>>>>>> I load up the old workspaces
>>>>>>>>>> and I enter
>>>>>>>>>>
>>>>>>>>>>> write.exprs(ABeset_gcrma, file="ABeset_gcrma081028orig.txt")
>>>>>>>>>> Where ABeset_gcrma is an old file
>>>>>>>>>>
>>>>>>>>>> and I get
>>>>>>>>>> Error in function (classes, fdef, mtable) :
>>>>>>>>>> unable to find an inherited method for function "write.exprs", for
>>>>>>>>>> signature
>>>>>>>>>> "exprSet"
>>>>>>>>>>
>>>>>>>>> It was probably more than a year ago - the exprSet class was
>>>>>>>>> deprecated and subsequently made defunct.
>>>>>>>>>
>>>>>>>>> You could try to do:
>>>>>>>>> library(Biobase)
>>>>>>>>>
>>>>>>>>> updateObject(ABeset_gcrma)
>>>>>>>>>
>>>>>>>>> failing that, you can try something like
>>>>>>>>> write.table(ABeset_gcrma at exprs,
>>>>>>>>> file="ABeset_gcrma081028orig.txt",uote = FALSE, sep = "\t",
>>>>>>>>> col.names = NA)
>>>>>>>>>
>>>>>>>>> or something like that.
>>>>>>>>>
>>>>>>>>>> And I enter
>>>>>>>>>>> exprs2excel(ABeset_gcrma, file="ABeset_gcrma081028v2.csv")
>>>>>>>>>> And I get
>>>>>>>>>> Error: could not find function "exprs2excel"
>>>>>>>>> That function has been made defunct.
>>>>>>>>>> Am I doing something wrong?
>>>>>>>>> No, you just can't expect that things won't change.
>>>>>>>>>
>>>>>>>>> best wishes
>>>>>>>>> Robert
>>>>>>>>>
>>>>>>>>>> Thank you
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioconductor mailing list
>>>>>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>>>> Search the archives:
>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Robert Gentleman, PhD
>>>>>>>>> Program in Computational Biology
>>>>>>>>> Division of Public Health Sciences
>>>>>>>>> Fred Hutchinson Cancer Research Center
>>>>>>>>> 1100 Fairview Ave. N, M2-B876
>>>>>>>>> PO Box 19024
>>>>>>>>> Seattle, Washington 98109-1024
>>>>>>>>> 206-667-7700
>>>>>>>>> rgentlem at fhcrc.org
>>>>>>>> _______________________________________________
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>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>> Search the archives:
>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
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>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>
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