[BioC] Choosing the transcripts for dataanalysis from GeneChip

[James W. MacDonald]

Hi Antony,

John Antonydas Gaspar wrote:
> Dear Sir/Madam,
> 
> I am just introduced to Affymetrix GeneChip technology and am supposed to do the
> analysis.
> 
> I just readin the .cel files:
> a-MHC A.cel,
> a-MHC B.cel,
> a-MHC C.cel,
> 
> ctrl-mES-02.cel,
> ctrl-mES-02.cel,
> ctrl-mES-03.cel.
> 
> Saved in a directory;
> 
> ibrary(affy)
> 
> Data <- ReadAffy()
> 
> list.celfiles()  # to show the CEL files that are locatd in currentworking
> directory
> 
> # CDF package automatically loaded contains the information about the PM and MM
> 
> eset_mas5 <- mas5(Data)
> 
> write.exprs(eset_eset_mas5, file="Data_all.xls")
> 
> 
> 
> Here in the Excel table I have tow coloumns for each condition that are
> Avg-signal value and the detection call.
> 
> Based on the detection call, I wished to filter the genes that is with
> P(Present) of the detection call. However for a single transcript in three
> chips(conditions) they are considered to be Present but at the rest they are
> with Absent call. Now how shall I go about in dealing with those transcripts
> with these behaviour?.

You keep them. Really the only transcripts you want to remove are those 
that are absent in _all_ conditions. The transcripts that are absent in 
some but not all conditions are usually the ones you are most interested in.

Best,

Jim


> 
> Kindly guide me if there is any special way to solve it.
> 
> 
> With Kind regards,
> 
> antony
> 
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826