I am new to the Exon array concept. I am trying to analyze
Mouse Exon 1.0 st array data using aroma.affymetrix and FIRMA model.
Few questions i have are below.

1) To get a start i have just implemented the code described in
vignette  "FIRMA: Human exon array analysis. " There are certain .CEL
files and other extension files generated. How can i read them into
R ? How do i know what information they carry ? Is there any other
software i can upload them to read these files ? How do i get control
of the analysis in applying extractMatrix() or extractDataFrame() ,
readUnits() functions ?

2)  I am unable to get a clear understanding of what the background
calculation are taking place using the functions ( used to generate
the files in Q.1) ? Except that these function performs QC,
Normalization, Summarization etc. I am lacing clear understanding how
those methods are implemented on Exon arrays , when compared to 3'
prime arrays ? for instance,, In 3'-IVT arrays, I have the control of
Normalizing within the group or across the group, where as in this
exon array analysis I'm not sure what the function does ?

3) I am not sure what other applications i can use with the end result
of  summarization / FIRMA. can i get a list of differentially
expressed genes ? splicing variant list ? upload the list of genes
into pathway studio for further analysis ? What methods should i use ?
can i use similar statistics that i use for 3' IVT arrays ? ( t-test,
Bonferroni etc. ?)

Please enlighten me a bit on this exon array analysis

Thank you,

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