[BioC] question about splice index in oneChannelGUI

[rcaloger]

Il 17/07/2011 12:00, bioconductor-request at r-project.org ha scritto:
> Message: 6
> Date: Sat, 16 Jul 2011 17:00:45 +0200
> From: frank blanchard<frnkblanchard at gmail.com>
> To:bioconductor at r-project.org
> Subject: [BioC] question about splice index in oneChannelGUI
> Message-ID:
> 	<CALnZ0kvkgpTOmh2jRLX7UvbH6K17V75gBH-HEnpFXojUyZ_ZBw at mail.gmail.com>
> Content-Type: text/plain
>
> Dear List
> Please someone could give to me details about how the splice index is
> calculated in oneChannelGUi?
> I'm checking some of the splice indexes calculated by this package (on exon
> arrays from 11 tissues available on affymetrix web site). But it seems to me
> that the splice indexes doesn't correspond to the output of the formula :
> log2 (expr exon probeset/expr transcript).
>
> For example:
>
> exon probeset 3832332 expr (in one tissue)                    2.55863
> transcript cluster ID 3832322 expr(in the same tissue)   4.47946
> splice index (computed by oneChannel)                           -1.92083
> splice index (computed with the formula previously reported)   -0.24321
>
> where i'm doing wrong?
> Thank you very much for any kind of help
> Frank
>
> 	[[alternative HTML version deleted]]
>
>
Dear Frank,
I am the maintainer of oneChannelGUI.
The splice index in oneChannelGUI is calculated by the formula log2 
(expr exon probeset/expr transcript)
I will check for the discrepancy you have found today and report the 
result on the mailing list.
Cheers
Raffaele

-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
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email: raffaele.calogero at unito.it
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