[BioC] Adding annotations to fit2

[Cei Abreu-Goodger]

Hi Sally,

You could also try adding your annotation to fit2$genes, which is where 
probe annotation is usually stored.

Cheers,

Cei

James MacDonald wrote:
> Hi Sally,
> 
> Your fit2 object is of class MArrayLM, whereas MGLnew is a data.frame, so there is no clear path to merge the two (in general, I believe merge() expects things of the same class, probably data.frame).
> 
> You might have better luck writing out your fit2 object using write.fit(), then reading back in using read.table(). This will give you a data.frame that you could then probably merge() with your MGLnew data.frame.
> 
> Best,
> 
> Jim
> 
> 
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
>>>> "Sally" <sagoldes at shaw.ca> 02/16/09 10:35 PM >>>
> I want merge fit2 with a txt file I'll call MGL (mastergenelist) which contains gene id information.  I am using a custom cDNA array.  The reason is that I want the gene ID information along-side the rownames (which are the accession IDs).  Both have identical row names.  MGL has missing data.
> 
> I have tried:
> 
> MGLnew<-read.table(file="MGL.txt",sep="\t",header=TRUE,na.strings="",fill=TRUE)  #WORKS
> write.table(MGLnew,file="MGLnew.txt",sep="\t") #WORKS
> fit2<-merge(fit2,MGLnew,by="row.names")  #NOT WORKING
> 
> When I run this I get the following error message:
> 
> Error in dim(data) <- dim : attempt to set an attribute on NULL
> 
> What does this error message mean?  How do I fix the problem?
> 
> Sally Goldes
> 
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> 
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