[BioC] Choosing the transcripts for dataanalysis from GeneChip

Bjoern Usadel Usadel at mpimp-golm.mpg.de
Wed Mar 4 18:40:21 CET 2009


Just make sure in your interpretation that you dont get inflated fold changes as mas5 can give you very low expression estimates which get highly negative values on the log scale.

I would also suggest to use (gc)rma by default if you are new to microarray analysis.

Best wishes

----- Originalnachricht -----
Von: bioconductor-bounces at stat.math.ethz.ch <bioconductor-bounces at stat.math.ethz.ch>
An: bioconductor at stat.math.ethz.ch <bioconductor at stat.math.ethz.ch>
Gesendet: Wed Mar 04 17:03:30 2009
Betreff: [BioC] Choosing the transcripts for dataanalysis from GeneChip

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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