[BioC] array names in arrayQualityMetrics report

[rchavez]

Hello,

My reports do not have the column "sampleNames":
http://132.248.224.66/~elizabeth/quality/

I use arrayQualityMetrics version 3.8.0 and R 2.13.1.

Am I missing something? A library when the package is built?


---------------
Message: 12
Date: Fri, 16 Sep 2011 18:52:44 +0200
From: Wolfgang Huber <whuber at embl.de>
To: bioconductor at r-project.org
Subject: Re: [BioC] array names in arrayQualityMetrics report
Message-ID: <4E737EDC.5010905 at embl.de>
Content-Type: text/plain; charset=UTF-8; format=flowed

Dear Ricardo

thanks for your feedback. I am not quite sure what your problem is.
Here's a report produced by a recent version of arrayQualityMetrics
http://www-huber.embl.de/users/whuber/bioc-list/110916/Report_for_nCCl4_with_RIN/
(the code for making it is in the package vignette).

The report section "Array metadata and outlier detection overview" gives
the mapping between sample names (cel file names) and numbers. Note that
by clicking on the section title you can expand or collapse the table.

The sample names (or cel file names) can be very long and would mess up
most of the plots.

Do this address your problem? Otherwise, can you precisify it?

    Wolfgang


Sep/14/11 5:06 PM, rchavez scripsit::
> Hello,
>
> The latest version of arrayQualityMetrics names the arrays "1, 2,
3...".
> How do I know which number corresponds to which .cel file? In previous
> versions the name was the .cel file name. Why the change?
>
> ---
> Dr. Ricardo A. Ch?vez Montes
> Laboratorio Nacional de Genomica para la Biodiversidad
> CINVESTAV-IPN
> Km. 9.6 Libramiento Norte, Carretera Irapuato-Le?n,
> A.P. 629, CP 36821, Irapuato, Guanajuato,
> Mexico
> Phone: +52 (462) 1663000 ext. 3011
> Fax: +52 (462) 6245846
> rchavez at langebio.cinvestav.mx


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