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

[Peng Yu]

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