Splicing index exon inclusion when doing ASPIRE

[A.Domingues]

Hi all,

I have a quick/simple question relating to the outpup files. I've
performed an ASPIRE analysis of a mouse JAY array in its simplest
form, that is, 3x experiment vs 3x control with the default settings.
Amongst other files, in the folder /AltResults/AlternativeOutput there
are 2 result files:

Mm_Junction_experiment_vs_control.p5_average-ASPIRE-exon-inclusion-
results.txt Mm_Junction_experiment_vs_controlp5_average-splicing-index-
exon-inclusion-results.txt

Does this mean that everytime ASPIRE is run Altanalize also calculates
linear regreassion analysis (splicing index file)?

Also I was trying to find an explanation for the meaning of these
values in the ASPIRE output file and which of these represent the
variation of a given splicing event in the condition vs control, for
instance "exon X is 20% more included compared to control":
ASPIRE
probeset1
norm-p1
probeset2
norm-p2
fold1
fold2
adj-fold1
adj-fold2

I am sure this is pretty straightforward but I have tried to figure it
out from the manual and couldn't.

Cheers,
António

[Nathan Salomonis]

Hi Antonio,

When you analyze a junction array or RNA-Seq three main files are produced:
1) Reciprocal junction results (ASPIRE or LinearRegression)
2) Individual exon or junction-level (splicing-index or FIRMA)
3) Comparison-evidence file which combines the two above to indicate which alternative exons have independent support evidence of regulation from both an alternative exon and two reciprocal junctions. The last provides some of the most confident results for validation.

Check out the following FAQ page:
http://code.google.com/p/altanalyze/wiki/FAQ

The most relevant page is below, which has a new example Excel file describing the fields in those result files:
http://code.google.com/p/altanalyze/wiki/ProteinDirectionIndicator

Best,
Nathan

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[António Miguel de Jesus Domingues]

Hi Nathan,

I id find the excel file with the explanation but for a previous version of AltAnalyze but the one that you indicate clears up my doubts.

Thanks a lot for your help!

António

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António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domi...@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology