[BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Sat Apr 8 01:22:23 CEST 2006

Dera group, 
limma is an excellent module for gene expression data
preprocessing and analysis.  
however, I looked into many places i did not find a
good tutorial when the .gpr file is not what I it
should look like. Also, when GAL file is not the same
what it should be. 

I have a dataset downloaded from ArrayExpress and has
the following column names:

[B635+1SD	B635+2SD	Autoflag	B Pixels	B635	B635 CV	B635
Mean	B635 Median	B635 SD	Circularity	Dia.	F Pixels
F635 % Sat.	F635 CV	F635 Mean	F635 Mean - B635	F635
Median	F635 Median - B635	F635 SD	F635 Total Intensity
Flags	Normalize	SNR 635]

The chip definition file obtained from "Array design
used" section of ArrayExpress has the following

[MetaColumn	MetaRow	Column	Row	Reporter Identifier
Reporter Name	Reporter Biosequence Type	Reporter
actual Sequence	Reporter Comment	Reporter Group Role
Reporter Control Type	CompositeSequence Identifier
CompositeSequence Name	Composite Sequence Comment]

when i did:
dat <- read.maimages('filename',source

I get "Error in readGPRHeader(fullname) : File is not
in Axon Text File (ATF) format"

my questions are:

what should I tell read.maimages to accept my file and
process further. 

what should I do when I do not have GAL file.  how can
the other file help me get genelist etc. 

Please help me. 


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