[BioC] Problems annotating a gene list

[Sean Davis]

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