[BioC] oneChannelGUI and hugene10stv1cdf

[rcaloger]

Dear Steve
I suggest you to download the latest version of oneChannelGUI 1.6.2
Due to various problems with cdfs I moved, in the latest version of oneChannelGUI, to the use of APT tools for the calculation of probe set summaries also for gene arrays.

You have to install by yourself APT tools on your computer. Than using the function "oneChannelGUI: Set Affymetrix apt tools folder" located in the general menu you will set the apt tool parameter in oneChannelGUI. Subsequently with the function "oneChannelGUI: Set library folder and install Affy gene/Exon library files" you will install in the oneChannelGUI dir all the Affymetrix library files needed to analyze gene and exon arrays.

There is in "file" menu a specific radio button for GENE arrays. 
Ones summaries are calculated those are stored in an ExpressionSet object and you can analyze them using any of the statistical tools interfaced in oneChannelGUI.

Let me know if you get any further problem in running the gene array analysis
Cheers
Raffaele
 

>#####################
>Hi,

>I am trying to run oneChannelGUI, analysing data based on the Affy Gene 1.0 ST Array.

>I installed the library from http://www.bioinformatica.unito.it/downloads/hugene10stv1cdf_1.0.0.tar.gz (I >am not sure how legitimate this is  :-)  ).

>When running the 'Table of genes ranked in order of differential expression' option in oneChannelGUI it >generated several errors (in the tcl/tk interface,see below) and wouldn't generate the top table 
>of results. It looks like it is trying to load 'hugene10stv1' rather than 'hugene10stv1cdf'. If this is >the problem, is there a workaround or an official hugene10stv1 library that works with this package?


----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
www:   www.bioinformatica.unito.it