[BioC] array names in arrayQualityMetrics report

[Wolfgang Huber]

Dear Ricardo

I have changed (improved) the default settings for this, if you use  the 
version from the devel branch, >=3.9.3, then the CEL file names will be 
there.

Alternative, you can always add whatever information you want displayed 
as additional columns to the phenoData slot of the ExpressionSet or 
AffyBatch.

	Hope this helps
	Wolfgang


Sep/17/11 10:05 PM, rchavez scripsit::
> 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
>
>


-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber