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]]

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 Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0116706487 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it

Hi Frank, getting back your question on splice index in oneChannelGUI I checked the code and, since exon probe sets and gene probe sets are log2 transformed in oneChannelGUI, the splice index is given by the difference between the log2 transformation of the intensities: log2(exon intensity) - log2(transcript intensity) = 2.55863 - 4.47946 = -1.92083 Cheers Raffaele Date: Mon, 18 Jul 2011 09:49:23 +0200 > From: rcaloger<raffaele.calogero at="" unito.it=""> > To: bioconductor at r-project.org, frnkblanchard at gmail.com > Subject: Re: [BioC] question about splice index in oneChannelGUI > Message-ID:<4E23E583.7050105 at unito.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 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 Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0116706487 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it