[BioC] Choosing the transcripts for dataanalysis from GeneChip

John Antonydas Gaspar gasparj at uni-koeln.de
Wed Mar 4 17:03:30 CET 2009

Dear Sir/Madam,

I am just introduced to Affymetrix GeneChip technology and am supposed to do the

I just readin the .cel files:
a-MHC A.cel,
a-MHC B.cel,
a-MHC C.cel,


Saved in a directory;


Data <- ReadAffy()

list.celfiles()  # to show the CEL files that are locatd in currentworking

# 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?.

Kindly guide me if there is any special way to solve it.

With Kind regards,


John Antonydas Gaspar,
Phd Student AG: Prof.A.Sachinidis
Institute of Neurophysiology
University of Cologne
Robert-Koch-Str. 39
50931 Cologne/Germany

Tel:  004922125918042
Handy:   004917683142627

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