[BioC] Does old workspace work?

Loren Engrav engrav at u.washington.edu
Fri Oct 31 17:58:48 CET 2008 

Got it, thank you
So the new ExpressionSets are Ok, cool
But one thing as I am still exploring the old data and the new
If I do show(obj) with the old exprSet I can see the data in the file
If I do show(obj) with the new ExpressionSet I just get a summary
How do I show(obj) and see the data in the new ExpressionSet
I checked ?show and google but could not find the answer

> 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



> From: Martin Morgan <mtmorgan at fhcrc.org>
> Date: Thu, 30 Oct 2008 15:42:44 -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:
>> 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
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>>> -----BEGIN PGP SIGNATURE-----
>>>>> Version: GnuPG v2.0.9 (GNU/Linux)
>>>>> Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org
>>>>> 
>>>>> iEYEARECAAYFAkkHYKAACgkQ6fE3kSKck1NjswCfQmXWj+2ny14EFrCB+4eNinxo
>>>>> kOkAnRAK5j9/K01A3zHf80OR2akCmL6P
>>>>> =NtCJ
>>>>> -----END PGP SIGNATURE-----
>>>> _______________________________________________
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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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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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