[BioC] Problems annotating a gene list

[Quentin Anstee]

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 guess I must have missed out a step but I'm not sure where I have gone
wrong. Any advice much appreciated.

Best wishes,

Quentin