I am trying to analyze Mouse Exon 1.0 st array data using
aroma.affymetrix and FIRMA model to find the splicing variants.
CDF file : MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf  ( downloaded from
the aroma.affymetrix website)
CEL files: 12 Mouse Exon 1.0 st arrays. ( 6 arrays for each strain A
and B) and Within A and B, i have 3 arrays each of two experimental

1) I am  not sure how the RMA normalization in aroma.affymetrix
performs, is the normalization performed within array or between the
array ? How do i pass arguments to the function to control the process
of normalization ?

2) What are .js and .css files generated at the end of the analysis
described in vignette ( Human Exon array ). Are there any third party
software that could be used to analyze this out put ?

3) How do i convert the probe set ID or transcript ID into gene name ?
Can i calculate the fold change in aroma.affymetrix ?

Thank you,

On Jul 27, 11:52 am, Sundar <sundar...@gmail.com> wrote:
> Hi,
>          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,
> Sundar

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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