Advanced spot quality analysis in two-colour microarray experiments.

Advanced spot quality analysis in two-colour microarray experiments. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Advanced spot quality analysis in two-colour microarray experiments. Abstract Text:

ABSTRACT: BACKGROUND: Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. FINDINGS: We evaluated the performance of two image analysis packages MAIA and GenePix (GP) using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5%) than GP with default spot filtering conditions. CONCLUSION: Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.

Advanced spot quality analysis in two-colour microarray experiments. Publishing Authors By Initials

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Advanced spot quality analysis in two-colour microarray experiments. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: BMC research notes

VOLUME: 1

Page Numbers: 80

Journal Abbreviation: BMC Res Notes

ISSN: 1756-0500

DAY: 17

MONTH: 09

YEAR: 2008

Advanced spot quality analysis in two-colour microarray experiments. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 101462768

Advanced spot quality analysis in two-colour microarray experiments. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: Advanced spot quality analysis in two-colour microarray experiments. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Advanced spot quality analysis in two-colour microarray experiments.

AFFILIATION: Microarray Center/LBMAGM, CRP-Santé, 84 Rue Val Fleuri, L-1526, Luxembourg. evelyne.friederich@uni.lu.

Country: England

AGENCY:

GRANT:

ACRONYM:

MEDLINETA: BMC Res Notes

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Advanced spot quality analysis in two-colour microarray experiments Related Publications

• Actin-filament cross-linking protein T-plastin increases Arp2/3-mediated actin-based movement.
• Advanced spot quality analysis in two-colour microarray experiments.
• Anorexia nervosa: selective processing of food-related word and pictorial stimuli in recognition and free recall tests.
• Biochemical and physiological parameters on the healthy skin surface of persons with candidal intertrigo and of persons with tinea cruris.
• Biochemical and physiological particularities on the skin surface of diabetics.
• Comparison of Sagittal and Frontal Plane Alignment After Open- and Closed-wedge Osteotomy: a Matched-pair Analysis.
• Lateral ankle fracture with missed proximal tibiofibular joint instability (Maisonneuve injury).
• Predisposing factors of the skin surface in persons with impetigo contagiosa.
• Predisposing factors on the surface of the skin in persons with pityriasis versicolor.
• [After care in malignant skin tumors]
• [Autologous cartilage transplantation--the future in arthrosis therapy?]
• [Cerebral tumor in infant.]
• [Comparative studies on the strength and elongation of the human hair.]
• [Femoropatellar pain syndrome: which operation is still sensible?]
• [Modifications of the cuticula of human hair due to the effects of radiations and shampoos.]
• [Not Available.]
• [Not Available.]
• [Perioperative pharmacological myocardial protection : Systematic literature-based process optimization.]
• [Physiotherapy in the acute phase of poliomyelitis.]
• [Surgical therapy of alopecias]