Reducing the Variability in cDNA Microarray Image Processing by Bayesian Inference

[edit]

Neil D. Lawrence, University of Sheffield
Marta Milo, University of Sheffield
Mahesan Niranjan, University of Southampton
Penny Rashbass
Stephan Soullier

Bioinformatics 20, pp 518-526

Related Material

Abstract

Motivation: Gene expression levels are obtained from microarray experiments through the extraction of pixel intensities from a scanned image of the slide. It is widely acknowledged that variabilities can occur in expression levels extracted from the same images by different users with the same software packages. These inconsistencies arise due to differences in the refinement of the placement of the microarray ‘grids’. We introduce a novel automated approach to the refinement of grid placements that is based upon the use of Bayesian inference for determining the size, shape and positioning of the microarray ‘spots’, capturing uncertainty that can be passed to downstream analysis.\ \ Results: Our experiments demonstrate that variability between users can be significantly reduced using the approach. The automated nature of the approach also saves hours of researchers’ time normally spent in refining the grid placement.\ \ Availability: A MATLAB implementation of the algorithm and an image of the slide used in our experiments, as well as the code necessary to recreate them are available for non-commercial use from http://inverseprobability.com/vis.


@Article{lawrence-variability03,
  title = 	 {Reducing the Variability in cDNA Microarray Image Processing by Bayesian Inference},
  journal =  	 {Bioinformatics},
  author = 	 {Neil D. Lawrence and Marta Milo and Mahesan Niranjan and Penny Rashbass and Stephan Soullier},
  pages = 	 {518},
  year = 	 {2004},
  volume = 	 {20},
  number =       {4},
  month = 	 {00},
  edit = 	 {https://github.com/lawrennd//publications/edit/gh-pages/_posts/2004-01-22-lawrence-variability03.md},
  url =  	 {http://inverseprobability.com/publications/lawrence-variability03.html},
  abstract = 	 {**Motivation:** Gene expression levels are obtained from microarray experiments through the extraction of pixel intensities from a scanned image of the slide. It is widely acknowledged that variabilities can occur in expression levels extracted from the same images by different users with the same software packages. These inconsistencies arise due to differences in the refinement of the placement of the microarray ‘grids’. We introduce a novel automated approach to the refinement of grid placements that is based upon the use of Bayesian inference for determining the size, shape and positioning of the microarray ‘spots’, capturing uncertainty that can be passed to downstream analysis.\
\
**Results:** Our experiments demonstrate that variability between users can be significantly reduced using the approach. The automated nature of the approach also saves hours of researchers’ time normally spent in refining the grid placement.\
\
**Availability:** A MATLAB implementation of the algorithm and an image of the slide used in our experiments, as well as the code necessary to recreate them are available for non-commercial use from .},
  key = 	 {Lawrence-variability03},
  doi = 	 {10.1093/bioinformatics/btg438},
  linkpsgz =  {ftp://ftp.dcs.shef.ac.uk/home/neil/microarrayImage.ps.gz},
  linksoftware = {http://inverseprobability.com/vis/},
  group = 	 {shefml,mig,puma}
 

}
%T Reducing the Variability in cDNA Microarray Image Processing by Bayesian Inference
%A Neil D. Lawrence and Marta Milo and Mahesan Niranjan and Penny Rashbass and Stephan Soullier
%B 
%C Bioinformatics
%D 
%F lawrence-variability03
%J Bioinformatics	
%P 518--526
%R 10.1093/bioinformatics/btg438
%U http://inverseprobability.com/publications/lawrence-variability03.html
%V 20
%N 4
%X **Motivation:** Gene expression levels are obtained from microarray experiments through the extraction of pixel intensities from a scanned image of the slide. It is widely acknowledged that variabilities can occur in expression levels extracted from the same images by different users with the same software packages. These inconsistencies arise due to differences in the refinement of the placement of the microarray ‘grids’. We introduce a novel automated approach to the refinement of grid placements that is based upon the use of Bayesian inference for determining the size, shape and positioning of the microarray ‘spots’, capturing uncertainty that can be passed to downstream analysis.\
\
**Results:** Our experiments demonstrate that variability between users can be significantly reduced using the approach. The automated nature of the approach also saves hours of researchers’ time normally spent in refining the grid placement.\
\
**Availability:** A MATLAB implementation of the algorithm and an image of the slide used in our experiments, as well as the code necessary to recreate them are available for non-commercial use from .
TY  - CPAPER
TI  - Reducing the Variability in cDNA Microarray Image Processing by Bayesian Inference
AU  - Neil D. Lawrence
AU  - Marta Milo
AU  - Mahesan Niranjan
AU  - Penny Rashbass
AU  - Stephan Soullier
PY  - 2004/01/22
DA  - 2004/01/22	
ID  - lawrence-variability03	
SP  - 518
EP  - 526
DO  - 10.1093/bioinformatics/btg438
UR  - http://inverseprobability.com/publications/lawrence-variability03.html
AB  - **Motivation:** Gene expression levels are obtained from microarray experiments through the extraction of pixel intensities from a scanned image of the slide. It is widely acknowledged that variabilities can occur in expression levels extracted from the same images by different users with the same software packages. These inconsistencies arise due to differences in the refinement of the placement of the microarray ‘grids’. We introduce a novel automated approach to the refinement of grid placements that is based upon the use of Bayesian inference for determining the size, shape and positioning of the microarray ‘spots’, capturing uncertainty that can be passed to downstream analysis.\
\
**Results:** Our experiments demonstrate that variability between users can be significantly reduced using the approach. The automated nature of the approach also saves hours of researchers’ time normally spent in refining the grid placement.\
\
**Availability:** A MATLAB implementation of the algorithm and an image of the slide used in our experiments, as well as the code necessary to recreate them are available for non-commercial use from .
ER  -

Lawrence, N.D., Milo, M., Niranjan, M., Rashbass, P. & Soullier, S.. (2004). Reducing the Variability in cDNA Microarray Image Processing by Bayesian Inference. Bioinformatics 20(4):518-526