[BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan

White, Peter Peter.White at nationwidechildrens.org
Fri Mar 12 16:22:40 CET 2010

Here is a plot made from data normalized with the limma package.

From: White, Peter
Sent: Friday, March 12, 2010 10:22 AM
To: 'bioconductor at stat.math.ethz.ch'
Subject: Issue with limma and normalization of Agilent data generated with a 20-bit scan

I have noticed an issue with the limma normalizeWithinArrays function (and also with marray and maNorm). When normalizing two color data generated with an Agilent 20-bt scanner it fails to normalize the high intensity data (i.e. any points with an A value > 16). In our dataset we have in excess of 400 elements with red and green intensities ranging from 65500 to 475100. When we loess normalize the data any points beyond A=16 appear to be untouched by the normalization. If the attached figures come through this should be clear - when using maNorm and maPlot it will plot the loess line and you can see it stop at 16.

Is it possible for loess normalization to be extended to this higher intensity data? Or am I just doing something wrong?



Peter White, Ph.D.
Director, Biomedical Genomics Core<http://genomics.nchresearch.org/>
Research Assistant Professor of Pediatrics
The Research Institute at
Nationwide Children's Hospital and
The Ohio State University

Mailing Address:

The Research Institute at
Nationwide Children's Hospital
700 Children's Drive, W510
Columbus, OH 43205

Assistant (Jennifer Neelans): (614) 722-2915
Office: (614) 355-2671
Lab: (614) 355-5252
Fax: (614) 722-2818
Web: http://genomics.nchresearch.org/

Confidentiality Notice: The following mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. The recipient is responsible to maintain the confidentiality of this information and to use the information only for authorized purposes. If you are not the intended recipient (or authorized to receive information for the intended recipient), you are hereby notified that any review, use, disclosure, distribution, copying, printing, or action taken in reliance on the contents of this e-mail is strictly prohibited. If you have received this communication in error, please notify Nationwide Children's Hospital immediately by replying to this e-mail and destroy all copies of the original message. Thank you.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: FoxD3 FoxD3_4 MvA Plots.png
Type: image/png
Size: 11628 bytes
Desc: FoxD3 FoxD3_4 MvA Plots.png
URL: <https://stat.ethz.ch/pipermail/bioconductor/attachments/20100312/a354da2a/attachment.png>

More information about the Bioconductor mailing list