Question

array names in arrayQualityMetrics report

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rchavez ▴ 20

@rchavez-4858

Last seen 9.7 years ago

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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

arrayQualityMetrics arrayQualityMetrics • 624 views

ADD COMMENT • link 12.6 years ago rchavez ▴ 20

score 0 · Answer 1 · 2011-09-16

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

score 0 · Answer 2 · 2011-09-17

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@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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.