[BioC] Does old workspace work?

[Loren Engrav]

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Is the file at the url below current, or out of date?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#BioC
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If it is out of date, is there a better url to catch up fast?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?
> 
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> 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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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
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