Harshlight: a "corrective make-up" program for microarray chips.
BMC Bioinformatics
; 6: 294, 2005 Dec 10.
Article
em En
| MEDLINE
| ID: mdl-16336691
ABSTRACT
BACKGROUND:
Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects.RESULTS:
We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip.CONCLUSION:
We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Biologia Computacional
/
Análise de Sequência com Séries de Oligonucleotídeos
Tipo de estudo:
Risk_factors_studies
Limite:
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2005
Tipo de documento:
Article
País de afiliação:
Estados Unidos