I am a Chinese student, English is not very good, some places may not be clear, I hope you can understand 

Recently, I've been using oligo packages to analyze Affymetrix Mouse Gene 2 .0 ST Array chips. But I'm not going to convert the probe's ID into the ID of the gene. This problem has been bothering me for a long time. I checked some information and didn't solve it. Is there anyone who can help me? Thank you very much .

Here's the code I'm using ：

library(oligo)

celFiles <- list.celfiles()

affyRaw <- read.celfiles(celFiles)

librarypd.mogene.2.0.st)

eset <- rma(affyRaw)

library(limma)

design <- model.matrix(~ 0+factor(c(1,1,1,2,2,2)))
colnames(design) <- c("group1", "group2")
contrast.matrix <- makeContrasts(contrasts="group2-group1",levels=design)
design
fit <- lmFit(eset, design)
fit1<- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit1)

dif<-topTable(fit2,coef="group2-group1",n=nrow(fit2),lfc=log2(2))
dif<-dif[dif[,"adj.P.Val"]<0.05,]
head(dif)

I can only do it here, how to do the ID conversion, I can not do it, can anyone help me, thank you again 

Most convenient would be using the function annotateEset() from the package affycoretools. Use as input the (your) normalized object eset. You can then annotate your dataset using either the corresponding pdInfo package, or the ChipDb package.

The annotation info available in the PdInfo package is basically a 1:1 copy of the info made available by Affymetrix on their support pages (in e.g. the file MoGene-2_0-st-v1.na36.mm10.transcript.csv). The the latter (ChipDb) is fully generated using the Bioconductor infrastructure; only the mapping probeset -> gene ID is extracted from the before-mentioned csv file. Thus:

library(affycoretools)

# using the PdInfo package
eset.anno1 <- annotateEset(eset, pd.mogene.2.0.st)

# using the ChipDb package
library(mogene20sttranscriptcluster.db)
eset.anno2 <- annotateEset(eset, mogene20sttranscriptcluster.db)

Then continue with the analysis in limma using the object eset.annox, the annotation info will be automagically added to the limma output.