[BioC] Inconsistency in RMA results from 'affy' and results from 'oligo'

[Peng Yu]

Hi,

I have run the two different R script to do RMA. Neither of them gives
me any error messages. However, the RMA results are very
different---they have very different number of lines. I don't know
which one I should believe. Or neither of them is correct. It might be
due to the difference in the cdf file used. Would you please point to
me how to figure out the problem?

$ Rscript probe2expr_affy.R
> library(affy)
Loading required package: Biobase
Loading required package: methods

Welcome to Bioconductor

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

> Data <- ReadAffy()
> eset <- rma(Data)
Background correcting
Normalizing
Calculating Expression
> write.exprs(eset, file="gene_expr_affy.txt", sep="\t")
>

$ Rscript probe2expr_oligo.R
> library(oligo)
Loading required package: oligoClasses
Loading required package: Biobase
Loading required package: methods

Welcome to Bioconductor

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

Loading required package: preprocessCore
Welcome to oligo version 1.8.1
> data<-read.celfiles(list.celfiles())
Loading required package: pd.mogene.1.0.st.v1
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : koA-mth_HZ_5238_MST1_19389.cel
Reading in : koB-mth_HZ_5238_MST1_19390.cel
Reading in : koC-mth_HZ_5238_MST1_19391.cel
Reading in : koD-mth_HZ_5238_MST1_19392.cel
Reading in : wt1-mth_HZ_5238_MST1_19385.cel
Reading in : wt2-mth_HZ_5238_MST1_19386.cel
Reading in : wt3-mth_HZ_5238_MST1_19387.cel
Reading in : wt4-mth_HZ_5238_MST1_19388.cel
> eset<-rma(data)
Background correcting
Normalizing
Calculating Expression
> write.exprs(eset, file="gene_expr_oligo.txt", sep="\t")
>

$ wc gene_expr_affy.txt gene_expr_oligo.txt
  34761   312848  5002519 gene_expr_affy.txt
 234591  2111318 33763075 gene_expr_oligo.txt
 269352  2424166 38765594 total

BTW, before I run 'Rscript probe2expr_affy.R'. I downloaded
MoGene-1_0-st-v1.r3.unsupported-cdf and I run the following script.
Then, I install the generated package 'mogene10stv1cdf'.
$ cat make_cdf_package.R
library(makecdfenv)
make.cdf.package("MoGene-1_0-st-v1.r3.cdf",
packagename="mogene10stv1cdf", species="Mus_musculus")

Regards,
Peng