[BioC] Problems annotating a gene list

[Quentin Anstee]

Hi Sean,

Thanks for coming back to me on this one. 

I have had a look at 'fit2$genes', all it contains are the affy probe IDs as
you predicted. Could you describe how to make the annotations and attach
them to the MArrayLM file or let me know where this process is described? I
have had a look in the limma help files and vignette but have not been able
to find a walk through of this procedure. 

Very many thanks,

Quentin


> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
> Sent: 24 February 2006 17:42
> To: Quentin Anstee; Bioconductor
> Subject: Re: [BioC] Problems annotating a gene list
> 
> 
> 
> 
> On 2/24/06 12:32 PM, "Quentin Anstee" <q.anstee at imperial.ac.uk> wrote:
> 
> > Dear List,
> >  
> > I am having some problems writing the contents of an 
> MArrayLM object 
> > to file and would be grateful for any help. I am processing 
> a 12 chip 
> > affy experiment in Bioconductor as follows:
> >  
> > Import .CEL files > GCRMA > Filter (kOverA & IQR) to 
> produce an eset 
> > file with 4000 probes called 'mySubSet' > Fit linear model 
> using the 
> > following script.
> >  
> > Libraries loaded:
> > 
> > library(simpleaffy)
> > library(genefilter)
> > library(geneplotter)
> > library(multtest)
> > library(affy)
> > library(limma)
> > library(gcrma)
> > library(xtable)
> > library(mouse4302)
> > library(mouse4302cdf)
> > library(annotate)
> > library(annaffy)
> > 
> > Script:
> > 
> > design <- model.matrix(~ -1+factor(c(1,1,1,1,2,2,2,3,3,3,3,3)))
> > colnames(design) <- c("A", "CONTROL", "B") fit <- lmFit(mySubSet, 
> > design) contrastNames<-c("A_CONTROL","B_CONTROL", "A_B") 
> > contrast.matrix <- makeContrasts(A-CONTROL, B-CONTROL, A-B, 
> > levels=design)
> > fit2 <- contrasts.fit(fit, contrast.matrix)
> > fit2 <- eBayes(fit2)
> > 
> write.fit(fit2,results=NULL,"Annotated_fit2_Table.txt",adjust="none")
> > 
> > When I output this table I have all the statistical data as 
> expected 
> > but not the gene names and annotation,etc that the help file says 
> > should also be included.
> 
> I think the help file does not include an "if available" for 
> the gene names and annotation, but it probably should, unless 
> I am mistaken.  I think you will have to make your own 
> annotation and attach it to the MArrayLM fit object or use 
> the limma data structures and attach it before running lmFit.
> 
> Sean
> 
>