Re: [base] Affymetrix Power Tools Error

Pharma AG, Werk Klybeck > NBx PROCESS DEV. BIOINFORMATIC > CHBS, WKL-681.1.10 > Klybeckstrasse 141 > CH-4057 Basel > Switzerland > Phone: +41 61 6962720 > Fax: +41 61 6963373 > Email : philipp-1.kai...@novartis.com > > > > > Jari Häkkinen > 04.03.

Re: [base] Affymetrix Power Tools Error

To BASE ML cc Subject Re: [base] Affymetrix Power Tools Error Hi, The problem seems to be in the apt-probeset-summarize program as you point out. Have you tried to run the same analysis outside of BASE? What is the outcome of that? Cheers, Jari philipp-1.kai...@novartis.com wrote:

Re: [base] Affymetrix Power Tools Error

Hi, The problem seems to be in the apt-probeset-summarize program as you point out. Have you tried to run the same analysis outside of BASE? What is the outcome of that? Cheers, Jari philipp-1.kai...@novartis.com wrote: > Hi, > > I am trying to get BASE 2.9.2 working with the APT 0.2 plugi

[base] Affymetrix Power Tools Error

Hi, I am trying to get BASE 2.9.2 working with the APT 0.2 plugin on a Testserver. Envorinment Condition are as follows: Windows XP Prof SP2, Tomcat 6, Affymetrix Powertools Version: apt-1.10.1-20081103 In some cases the Conversion of .CEL files to Probeset Signal worked, but most of the time

Re: [base] affymetrix

thanks to Dominic, Philippe & Nicklas for the informative replies. I'll take the external ontology thing off-list with the EBI guys and we'll report back as necessary. Nicklas Nordborg writes: > Bob MacCallum wrote: > > > > > Emmanuel Courcelle wrote: > > > > Hello > > > > > > > > Tr

Re: [base] affymetrix

Bob MacCallum wrote: > > > Emmanuel Courcelle wrote: > > > Hello > > > > > > Trying to use BASE with affymetrix data. > > me too! > > > > 2/ I can't see any new Reporter in the View/Reporters > > > > You need to import the reporter from a reporter annotation file (.csv). > > See >

Re: [base] affymetrix

Hello, Just a couple of things regarding using Affymetrix with BASE. i. We are just about to release a plugin to create ArrayDesigns from a bunch of zipped CDF files. This should speed up part of the process of managing Affymetrix Designs. Will post when ready. ii. I have a little simple perl

Re: [base] affymetrix

> Emmanuel Courcelle wrote: > > Hello > > > > Trying to use BASE with affymetrix data. me too! > > 2/ I can't see any new Reporter in the View/Reporters > > You need to import the reporter from a reporter annotation file (.csv). > See > http://lev.thep.lu.se/trac/baseplugins/brows

Re: [base] affymetrix

Emmanuel Courcelle wrote: > Hello > > Trying to use BASE with affymetrix data. > I think we missed something... but don't know what > > We have created: > -An array design called ATH1-121501, from the file ATH1-121501.CDF > -Several raw bioassays fro several .cel files, when I click on the > bio

[base] affymetrix

Hello Trying to use BASE with affymetrix data. I think we missed something... but don't know what We have created: -An array design called ATH1-121501, from the file ATH1-121501.CDF -Several raw bioassays fro several .cel files, when I click on the bioassays -An experiment connected to these bio

Re: [base] Affymetrix Format

ftware solution for instrument control and expression analysis (expression console) doesn't use CAB files any more it uses flat files. Hope this helps Ed -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jari Häkkinen Sent: 24 April 2007 11:17 To: BA

Re: [base] Affymetrix Format

There is no support for ddt or cab. Currently only cdf and cel files are supported by the Affymetrix plug-ins. Annotation files (.csv) are used for uploading probeset (reporter in BASE language) information. The issue of supporting ddt and cab files is an import and a plug-in issue. There are two

[base] Affymetrix Format

Hi I would know if it's possible to use dtt or cab format with BASE ? Regards -- Joel Masciocchi Engineer of Bioinformatics Service Line CRS4 - Bioinformatics Loc. Pixina Manna Edificio 3 Pula 09010 (CA), Italy - This SF