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

[Benilton Carvalho]

Dear Peng,

I can speak for oligo and the annotation package used by it.

The current release of oligo summarizes to the probeset level. The  
next release of oligo and annotation packages will allow you to  
summarize to the gene level. In your particular case, the count you'll  
get is roughly 35K.

The updated packages have already been submitted to BioC and soon  
should show up on the devel branch.

Best wishes,

b

On Aug 10, 2009, at 6:39 PM, Peng Yu wrote:

> 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
>
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