Assessing probe-specific dye and slide biases in two-color microarray data.
| Title: | Assessing probe-specific dye and slide biases in two-color microarray data. |
|---|---|
| Authors: | Lu R; Department of Data Analysis and Algorithm, Affymetrix, Inc., Santa Clara, California, USA. tinypenguin@gmail.com; Lee GC; Shultz M; Dardick C; Jung K; Phetsom J; Jia Y; Rice RH; Goldberg Z; Schnable PS; Ronald P; Rocke DM |
| Source: | BMC bioinformatics [BMC Bioinformatics] 2008 Jul 19; Vol. 9, pp. 314. Date of Electronic Publication: 2008 Jul 19. |
| Publication Type: | Evaluation Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S. |
| Language: | English |
| Journal Info: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [London] : BioMed Central, 2000- |
| MeSH Terms: | Algorithms*; DNA Probes/*genetics ; Fluorescent Dyes/*analysis ; Image Interpretation, Computer-Assisted/*methods ; Microscopy, Fluorescence, Multiphoton/*methods ; Oligonucleotide Array Sequence Analysis/*methods; Observer Variation ; Reproducibility of Results ; Sensitivity and Specificity |
| Abstract: | Background: A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any differences between the dyes can be adjusted out by standard methods of normalization, so that measures such as log ratios on the same slide are reliable measures of comparative expression. However, even after the normalization, there are still probe specific dye and slide variation among the data. We define a method to quantify the amount of the dye-by-probe and slide-by-probe interaction. This serves as a diagnostic, both visual and numeric, of the existence of probe-specific dye bias. We show how this improved the performance of two-color array analysis for arrays for genomic analysis of biological samples ranging from rice to human tissue.; Results: We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function), though numerical results are also obtained.; Conclusion: We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor. |
| References: | Bioinformatics. 2005 Jun 15;21(12):2803-4. (PMID: 15817695); Environ Health Perspect. 2004 Mar;112(4):480-7. (PMID: 15033598); Semin Cell Dev Biol. 2004 Dec;15(6):703-13. (PMID: 15561590); Bioinformatics. 2005 May 15;21(10):2430-7. (PMID: 15774555); FEBS Lett. 2004 Feb 27;560(1-3):120-4. (PMID: 14988009); J Comput Biol. 2000;7(6):819-37. (PMID: 11382364); Clin Cancer Res. 2006 Jun 15;12(12):3723-9. (PMID: 16778099); Biostatistics. 2007 Jan;8(1):128-39. (PMID: 16636140); Bioinformatics. 2005 Jul 15;21(14):3065. (PMID: 15941744); Bioinformatics. 2005 May 1;21(9):1995-2000. (PMID: 15691855); Methods Mol Biol. 2003;224:111-36. (PMID: 12710670); Radiat Res. 2006 Feb;165(2):240-7. (PMID: 16435922) |
| Grant Information: | R01-HG003352 United States HG NHGRI NIH HHS; P42-ES04699 United States ES NIEHS NIH HHS; P42 ES004699 United States ES NIEHS NIH HHS; R01 HG003352 United States HG NHGRI NIH HHS; P30 CA093373-04 United States CA NCI NIH HHS; P30 CA093373 United States CA NCI NIH HHS |
| Substance Nomenclature: | 0 (DNA Probes); 0 (Fluorescent Dyes) |
| Entry Date(s): | Date Created: 20080722 Date Completed: 20080910 Latest Revision: 20250529 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC2496918 |
| DOI: | 10.1186/1471-2105-9-314 |
| PMID: | 18638416 |
| Database: | MEDLINE |
Evaluation Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.