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

[Peng Yu]

Hi Benilton,

If both of scripts do not generate errors, does it mean that both of
them are correct? But the RMA results are very different, so one of
them must be wrong?

Regards,
Peng

On Mon, Aug 10, 2009 at 7:54 PM, Benilton Carvalho<bcarvalh at jhsph.edu> wrote:
> For the Mouse Gene ST Array, 'oligo' needs the "pd.mogene.1.0.st.v1"
> package. If it didn't complain about it when reading the CEL files, it's
> because you already had it installed on your system. The next version of
> 'oligo' will be able to identify the required package (as it does currently)
> and automatically download/install the required packages, if available on
> the BioC website.
>
> As a side note, please observe that the annotation packages used by 'affy'
> are not compatible with those used by 'oligo', which are built via
> 'pdInfoBuilder'.
>
> b
>
> On Aug 10, 2009, at 9:27 PM, Peng Yu wrote:
>
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>