[BioC] Does old workspace work?
Loren Engrav
engrav at u.washington.edu
Thu Oct 30 22:28:53 CET 2008
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?
> 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
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
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>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives:
>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>
>>>
>>>> _______________________________________________
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>>
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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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