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List:       bioconductor
Subject:    Re: [BioC] annotations of Human Gene 1.0 ST microarray and
From:       rcaloger <raffaele.calogero () gmail ! com>
Date:       2010-08-31 13:41:52
Message-ID: 4C7D06A0.5030501 () unito ! it
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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@ifi.csic.es
To:bioconductor@stat.math.ethz.ch
Subject: [BioC] annotations of Human Gene 1.0 ST microarray and
	oneChannelGUI
Message-ID:<20100829012100.lxz5k9x2i7koscgs@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@unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it

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