Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2006 Mar 1;7:100. doi: 10.1186/1471-2105-7-100

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

Copyright © 2006 Bengtsson and Hössjer; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Log-ratios versus log-intensities before and after a robust affine normalization. Log-ratios versus log-intensities before and after a robust affine normalization. Left: Non-normalized data. Spike-ins designed to have log₂r = +2, 0, and -2 are highlighted in red, yellow and green, respectively. Middle: Affine normalization utilizing constraint (32) resulting in no negative signals. Parameter estimates used in back transformation are ( ${\hat{a}}_{G}$ , ${\hat{a}}_{R}$ , log₂ $\hat{β}$ ) = (39.0, 22.0, -0.418). Right: Affine normalization where 5% (default) negative signals has been allowed; Parameter estimates used in back transformation are ( ${\hat{a}}_{G}$ , ${\hat{a}}_{R}$ , log₂ $\hat{β}$ ) = (45.7, 27.0, -0.418). The rotated binning effects of data points at low intensities are due to (unnecessary) rounding of average spot pixel intensity to nearest integer by the image analysis software.