[BioC] How to extract expressed genes from Affymetrix data

[michelle_low]

Hi all,
 
I have done the differential expression analysis below but I wanna know the total number of expressed genes/transcripts in each cell (wild type and the mir223 knockout cell). Can somebody help? Thanks in advance..
 
 
Regards,
Michelle
 
 
 
 R version 2.13.2 (2011-09-30)
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> library(affy)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

>  library(limma)
>  pd=read.AnnotatedDataFrame("phenodata.txt",header=TRUE,sep="",row.names=1)
> a=ReadAffy(filenames=rownames(pData(pd)),phenoData=pd,verbose=TRUE)
1 reading wildrep1.CEL ...instantiating an AffyBatch (intensity a 1004004x6 matrix)...done.
Reading in : wildrep1.CEL
Reading in : wildrep2.CEL
Reading in : wildrep3.CEL
Reading in : miR223rep1.CEL
Reading in : miR223rep2.CEL
Reading in : miR223rep3.CEL
>  x=rma(a)
Background correcting
Normalizing
Calculating Expression
> c=paste(pd$treatment,pd$n,sep="")
> f=factor(c)
> design=model.matrix(~0+f)
>  colnames(design)=levels(f)
> fit=lmFit(x,design)
> library(mouse4302.db)
Loading required package: AnnotationDbi
Loading required package: org.Mm.eg.db
Loading required package: DBI


> fit$genes$Symbol <- getSYMBOL(fit$genes$ID,"mouse4302.db")
Error: could not find function "getSYMBOL"
> library(annotate)
> fit$genes$Symbol <- getSYMBOL(fit$genes$ID,"mouse4302.db")
> contrast.matrix=makeContrasts(E="present-absent")
Error in .Internal(inherits(x, what, which)) : 'x' is missing
> contrast.matrix=makeContrasts(E="present-absent",levels=design)
> fit2=contrasts.fit(fit,contrast.matrix)
> fit2=eBayes(fit2)
> results1 <-topTable (fit2, coef=1, p.value=0.3,number=nrow(fit2))
> dim(results1)
[1] 889   8
> results1 <-topTable (fit2, coef=1, p.value=0.5,number=nrow(fit2))
> dim(results1)
[1] 2997    8
> results1 <-topTable (fit2, coef=2, p.value=0.5,number=nrow(fit2))
Error in toptable(fit = fit[c("coefficients", "stdev.unscaled")], coef = coef,  : 
  subscript out of bounds
> write.table(results1, file="WT-KO.txt")
> results1 <-topTable (fit2, coef=2, p.value=0.4,number=nrow(fit2))
Error in toptable(fit = fit[c("coefficients", "stdev.unscaled")], coef = coef,  : 
  subscript out of bounds
> results1 <-topTable (fit2, coef=1, p.value=0.4,number=nrow(fit2))
> dim(results1)
[1] 1668    8
> write.table(results1, file="WT-KO.txt")