[BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7

[rcaloger]

You are right, I check the object creation, it was July 2005, therefore 
it was created with the release 1.6 of Bioconductor.
This is the output of the class(tr7.rma)
[1] "exprSet"
attr(,"package")
[1] "Biobase"

I manage to see the content of the object with show(tr7.rma) also on 
Bioconductor 1.8.
However, the str(tr7.rma) gives the error

Error in FUN(X[[6]], ...) : no slot of name "reporterInfo" for this 
object of class "exprSet"


I have then created a new instace of exprSet in the following way:
pd.xx<-new("phenoData")
pData(pd.xx)<-pData(tr7.rma)
xx<-new('exprSet', exprs = exprs(tr7.rma), phenoData=pd.xx)
tr7.rma<-xx

I had to recreate also the phenoData instance since the varMetadata 
variable was missed in my phenoData.
However, this problem rise the question: is ti reasonable to use exprSet 
objects as backup?
Thanks for your help
Raffaele

 
Martin Morgan wrote:

>Raf --
>
>Can you provide just a bit more information? What's the result of
>
>  
>
>>class(tr7.rma)
>>    
>>
>
>Also, I suspect that tr7.rma was created not in the last release of
>Biobase, but the release before that (at least). I say this because
>the 'reporterInfo' slot was present in the 1.7 release.
>
>In the mean time, I suspect that
>
>  
>
>>show(tr7.rma)
>>    
>>
>
>will display the contents of your object.
>
>Martin
>
>rcaloger <raffaele.calogero at unito.it> writes:
>
>  
>
>>Hi,
>>today I was working on an Affy exprSet I saved before the new release of 
>>Bioconductor (1.8).
>>I loaded it but I got the following error when I tried to show it:
>>library(affy)
>>load("tr7.rma.rda")
>>tr7.rma
>>Error in slot(object, what) : no slot of name "pubMedIds" for this 
>>object of class "MIAME"
>>
>>Furthermore, if I issue the command:
>>str(tr7.rma)
>>I got this error:
>>Error in FUN(X[[6]], ...) : no slot of name "reporterInfo" for this 
>>object of class "exprSet"
>>
>>I was expecting that there should be some sort of back compatibility 
>>with  at least the previous release of the exprSet.
>>The error comes using the  Biobase Version: 1.10.0.
>> 
>>There is any way to fix the problem or Do I have to install again the 
>>old release of  Bioconductor?
>>Thanks
>>Raf
>>
>>
>>-- 
>>
>>----------------------------------------
>>Prof. Raffaele A. Calogero
>>Bioinformatics and Genomics Unit
>>Dipartimento di Scienze Cliniche e Biologiche
>>c/o Az. Ospedaliera S. Luigi
>>Regione Gonzole 10, Orbassano
>>10043 Torino
>>tel.   ++39 0116705420
>>Lab.   ++39 0116705408
>>Fax    ++39 0119038639
>>Mobile ++39 3333827080
>>email: raffaele.calogero at unito.it
>>www:   www.bioinformatica.unito.it
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>    
>>


-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705420
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   www.bioinformatica.unito.it