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

[James W. MacDonald]

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/

Best,

Jim


> 
> Regards,
> Peng
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826