[BioC] What should be the output after processing a cel file?

[Marc Carlson]

Hi Peng,

Based on the probe IDs you have shown us here, you want the 
'mogene10stprobeset.db' package for annotations.  Affymetrix did some
changes mid stream about what they were going to call an ID for that
platform and so we have to accommodate people both before and after said
changes.  This is why there are two variants of annotation packages for
that platform.

  Marc




Peng Yu wrote:
> On Fri, Jul 24, 2009 at 12:43 PM, James W.
> MacDonald<jmacdon at med.umich.edu> wrote:
>   
>> Hi Peng,
>>
>> Peng Yu wrote:
>>     
>>> Hi,
>>>
>>> I run the following command in R.
>>>
>>> library(oligo)
>>> data<-oligo::read.celfiles("some.cel")
>>> eset<-rma(data)
>>> write.exprs(eset, file="some.txt", sep="\t")
>>>
>>> It generate the file "some.txt". But I am not sure what it means. The
>>> content of some.txt is the following.
>>>
>>>        wt1-mth_HZ_5238_MST1_19385.cel
>>> 10344615        7.83088386872146
>>> 10344617        3.13300493228193
>>> 10344619        3.00984893419684
>>> 10344621        4.55830890064195
>>> 10344623        7.79420011157519
>>> 10344625        8.93864799064523
>>> 10344626        10.2404135279143
>>> 10344627        8.36493644804453
>>> 10344628        10.8239110733786
>>>
>>>
>>> I am wondering if I processed the cel file correctly. What does the
>>> first column mean?
>>>       
>> The first column is the affy probeset ID. You can use the correct annotation
>> package to map these IDs to more conventional IDs, such as Entrez Gene or
>> Ensembl using the correct .db package. Had you noted what chip this is, I
>> might have been able to point you to the correct chip. But you can peruse
>> this webpage to find it:
>>
>> http://www.bioconductor.org/packages/release/data/annotation/
>>     
>
> Hi Jim,
>
> It's the Mouse Gene 1.0 ST Array.
>
> http://www.affymetrix.com/products_services/arrays/specific/mousegene_1_st.affx
>
> The following is the output of my R script. Shall I use
> 'mogene10stprobeset.db' and 'mogene10sttranscriptcluster.db'?
>
> Regards,
> Peng
>
>   
>> library(oligo)
>>     
> Loading required package: oligoClasses
> Loading required package: Biobase
>
> 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
>   
>> for (f in c("wt1-mth_HZ_5238_MST1_19385",
>>     
> +  "wt2-mth_HZ_5238_MST1_19386",
> +  "wt3-mth_HZ_5238_MST1_19387",
> +  "wt4-mth_HZ_5238_MST1_19388",
> +  "koA-mth_HZ_5238_MST1_19389",
> +  "koB-mth_HZ_5238_MST1_19390",
> +  "koC-mth_HZ_5238_MST1_19391",
> +  "koD-mth_HZ_5238_MST1_19392"
> + )) {
> + data<-oligo::read.celfiles(paste(f, ".cel", sep=''))
> + eset<-rma(data)
> + write.exprs(eset, file=paste(f, ".txt", sep=''), sep="\t")
> + }
> Loading required package: pd.mogene.1.0.st.v1
> Loading required package: RSQLite
> Loading required package: DBI
> Platform design info loaded.
> Reading in : wt1-mth_HZ_5238_MST1_19385.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : wt2-mth_HZ_5238_MST1_19386.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : wt3-mth_HZ_5238_MST1_19387.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : wt4-mth_HZ_5238_MST1_19388.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : koA-mth_HZ_5238_MST1_19389.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : koB-mth_HZ_5238_MST1_19390.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : koC-mth_HZ_5238_MST1_19391.cel
> Background correcting
> Normalizing
> Calculating Expression
> Platform design info loaded.
> Reading in : koD-mth_HZ_5238_MST1_19392.cel
> Background correcting
> Normalizing
> Calculating Expression
>   
>> proc.time()
>>     
>    user  system elapsed
> 574.095  14.989 595.596
>
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