[BioC] annotations of Human Gene 1.0 ST microarray and oneChannelGUI

[rcaloger]

Dear Virginia,
I am the maintainer of oneChannelGUI.
oneChannelGUI summarize intensities using APT tools.
One of the important points, indicated in the installation instructions, is that R folder and your data folder
are without "space in the path", which are creating problems when the command for APT tool is executed by oneChannelGUI.

Please check if you have space in the above indicated paths and be sure that the working folder of oneChannelGUI is the one where the cel files are located.

If you are still having troubles please load oneChannelGUI and execute in the main R windows the following commands and send their output to me together with you target file:

affylmGUIenvironment$libDirLocation
affylmGUIenvironment$aptDir

getwd()
dir()

Cheers
Raffaele

Message: 13
Date: Sun, 29 Aug 2010 01:21:00 +0200
From:ifig319 at ifi.csic.es
To:bioconductor at stat.math.ethz.ch
Subject: [BioC] annotations of Human Gene 1.0 ST microarray and
	oneChannelGUI
Message-ID:<20100829012100.lxz5k9x2i7koscgs at webmail.csic.es>
Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
	format="flowed"


Dear list,

This is my first experience working on microarray data. I am trying to
analyze Human Gene 1.0 ST microarray data with oneChannelGUI. However,
this seems to be not a straightforward task. I have been playing
around with data and the application and I am a little bit confused
and without any result yet!

First, I installed all the packages and then, followed the user guide
instructions.
When I select "GENE 1.0 ST ARRAYS: probe sets summary from Affymetrix
APT" option to perform a new analysis, it asks me if I want to use APT
for gene/exon summaries. I click "yes" and chose the organisms (in my
case, Hs). Next, I select the working directory, the target file and
answer "no" to the question "are you using genechips version 1.1?".
Finally, as APT tool intensity summary option, I select "rma-sketch".
Inmmediatly, I get a series of error messages (see below).

I really do not know what is happening here. I would like to make the
background correction, normalization and summarization, and also run
limma.
On the other hand, I can load a normalized tab delimited data set and
apply some functions on it, but I do not know how to include the
annotations into the final list of differential expressed genes (top
table).
anybody has a suggestion about what is happening here and how could I
solve it?
I would appreciate your help.

Best regards and thank you in advance for your attention.
Virginia.

-------
R CONSOLE:

Gene level probe sets summary started

Gene level probe sets summary ended
Error en as.matrix(my.exons) :
    ninguna funci?n desde donde volver, saltando a nivel superior
Adem?s: Mensajes de aviso perdidos
1: In file(file, "rt") :
    s?lo fue usado el primer elemento del argumento 'description'
2: In system(gene.rma.sketch, wait = T) : C:/Archivos no encontrado
3: In file(file, "rt") :
    no fue posible abrir el archivo 'C:/onChannelGUI/out5f906952/': No
such file or directory

-- 

----------------------------------------
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