[BioC] Does old workspace work?

Loren Engrav engrav at u.washington.edu
Fri Oct 31 19:51:03 CET 2008


Actually exprs(obj) does show, indented, sorry


Thank you, got it

 exprs(obj) is missing from the output but shows in ?ExpressionSet and puts
up the data so I can see it

And now perhaps one final question to understanding this old data and
progress

Long long ago I did
AA_ReadAffy <- ReadAffy()
ABeset_gcrma < gcrma (AA_ReadAffy)

Now I do
AA_ReadAffy081031 <- ReadAffy() #on the same .cel files
ABeset_gcrma081031 <- gcrma (AA_ReadAffy081031)

Then I do
Show(ABeset_gcrma) and exprs(ABeset_gcrma081031)

And they do not match, for example
Probe set Ssc.10026.1.A1_at
ABeset_gcrma is 4.124689
ABeset_gcrma081031 is 3.344443

 ReadAffy changed?
 gcrma changed?



> From: Martin Morgan <mtmorgan at fhcrc.org>
> Organization: Fred Hutchinson Cancer Research Center
> Date: Fri, 31 Oct 2008 11:08:06 -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:
>> 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
> 
>> library(Biobase)
>> data(sample.ExpressionSet)
>> obj <- sample.ExpressionSet # easier to type#
>> obj
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 500 features, 26 samples
>    element names: exprs, se.exprs
> phenoData
>    sampleNames: A, B, ..., Z  (26 total)
>    varLabels and varMetadata description:
>      sex: Female/Male
>      type: Case/Control
>      score: Testing Score
> featureData
>    featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at  (500 total)
>    fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: hgu95av2
> 
> The output is meant to suggest how to access elements, e.g.,
> 
>> assayData(obj)
> <environment: 0xf00858>
>> assayData(obj)
> <environment: 0xf00858>
>> sampleNames(obj)
>   [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P"
> "Q" "R" "S"
> [20] "T" "U" "V" "W" "X" "Y" "Z"
>> phenoData(obj)
> An object of class "AnnotatedDataFrame"
>    sampleNames: A, B, ..., Z  (26 total)
>    varLabels and varMetadata description:
>      sex: Female/Male
>      type: Case/Control
>      score: Testing Score
> 
> details are on ?ExpressionSet and related classes.
> 
> Martin
> 
>>> 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
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>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
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>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
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>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>> -- 
>>>>> 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
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>> Search the archives:
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>> 
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> -- 
> 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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