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

[Peng Yu]

Hi Benilton,

One thing I don't understand isf why 'oligo' didin't require me to
install the .cdf file, but 'affy' required me to install the .cdf
file. I am curious that how 'oligo' figure how where the correct .cdf
file is and use it?

Regards,
Peng

On Mon, Aug 10, 2009 at 5:25 PM, Benilton Carvalho<bcarvalh at jhsph.edu> wrote:
> 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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>