共查询到20条相似文献,搜索用时 500 毫秒
1.
Background
Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip) is used to study protein-DNA interactions and histone modifications on a genome-scale. To ensure data quality, these experiments are usually performed in replicates, and a correlation coefficient between replicates is used often to assess reproducibility. However, the correlation coefficient can be misleading because it is affected not only by the reproducibility of the signal but also by the amount of binding signal present in the data. 相似文献2.
James J Chen Huey-Miin Hsueh Robert R Delongchamp Chien-Ju Lin Chen-An Tsai 《BMC bioinformatics》2007,8(1):412
Background
Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms. The MAQC analysis presented for the conclusion of inter- and intra-platform comparability/reproducibility of microarray gene expression measurements is inadequate. We evaluate the reproducibility/comparability of the MAQC data for 12901 common genes in four titration samples generated from five high-density one-color microarray platforms and the TaqMan technology. We discuss some of the problems with the use of correlation coefficient as metric to evaluate the inter- and intra-platform reproducibility and the percent of overlapping genes (POG) as a measure for evaluation of a gene selection procedure by MAQC. 相似文献3.
Nysia I George Joanne R Lupton Nancy D Turner Robert S Chapkin Laurie A Davidson Naisyin Wang 《BMC bioinformatics》2010,11(1):13
Background
Developing and evaluating new technology that enables researchers to recover gene-expression levels of colonic cells from fecal samples could be key to a non-invasive screening tool for early detection of colon cancer. The current study, to the best of our knowledge, is the first to investigate and report the reproducibility of fecal microarray data. Using the intraclass correlation coefficient (ICC) as a measure of reproducibility and the preliminary analysis of fecal and mucosal data, we assessed the reliability of mixture density estimation and the reproducibility of fecal microarray data. Using Monte Carlo-based methods, we explored whether ICC values should be modeled as a beta-mixture or transformed first and fitted with a normal-mixture. We used outcomes from bootstrapped goodness-of-fit tests to determine which approach is less sensitive toward potential violation of distributional assumptions. 相似文献4.
Purpose
For compliance with the ISO standard 14044, comparative life cycle assessments are required to address data quality for time-related coverage, geographic coverage, technology coverage, precision, completeness, representativeness, consistency, reproducibility, sources of the data and uncertainty of the information. As the community of practitioners and data developers grows, the purpose of this commentary is to initiate discussion of current issues and opportunities for improvement in data quality analysis. 相似文献5.
Background
The quality of microarray data can seriously affect the accuracy of downstream analyses. In order to reduce variability and enhance signal reproducibility in these data, many normalization methods have been proposed and evaluated, most of which are for data obtained from cDNA microarrays and Affymetrix GeneChips. CodeLink Bioarrays are a newly emerged, single-color oligonucleotide microarray platform. To date, there are no reported studies that evaluate normalization methods for CodeLink Bioarrays. 相似文献6.
Gerhard G Thallinger Kerstin Baumgartner Martin Pirklbauer Martina Uray Elke Pauritsch Gabor Mehes Charles R Buck Kurt Zatloukal Zlatko Trajanoski 《BMC bioinformatics》2007,8(1):81
Background
With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. 相似文献7.
Background
Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI) is a proteomics tool for biomarker discovery and other high throughput applications. Previous studies have identified various areas for improvement in preprocessing algorithms used for protein peak detection. Bottom-up approaches to preprocessing that emphasize modeling SELDI data acquisition are promising avenues of research to find the needed improvements in reproducibility. 相似文献8.
Background
Protein profiling with surface-enhanced laser desorption-ionisation time-of-flight mass spectrometry (SELDI-TOF MS) is a promising approach for biomarker discovery. Some candidate biomarkers have been identified using SELDI-TOF, but validation of these can be challenging because of technical parameters that effect reproducibility. Here we describe steps to improve the reproducibility of peak detection. 相似文献9.
Background
Gene expression signatures are typically identified by correlating gene expression patterns to a disease phenotype of interest. However, individual gene-based signatures usually suffer from low reproducibility and interpretability. 相似文献10.
Jorgen R Jepsen Lise H Laursen Carl-Goran Hagert Svend Kreiner Anders I Larsen 《BMC neurology》2006,6(1):8
Background
We have previously assessed the reproducibility of manual testing of the strength in 14 individual upper limb muscles in patients with or without upper limb complaints. This investigation aimed at additionally studying sensory disturbances, the mechanosensitivity of nerve trunks, and the occurrence of physical findings in patterns which may potentially reflect a peripheral neuropathy. The reproducibility of this part of the neurological examination has never been reported. 相似文献11.
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays 总被引:1,自引:0,他引:1
Background
Reproducibility of results can have a significant impact on the acceptance of new technologies in gene expression analysis. With the recent introduction of the so-called next-generation sequencing (NGS) technology and established microarrays, one is able to choose between two completely different platforms for gene expression measurements. This study introduces a novel methodology for gene-ranking stability analysis that is applied to the evaluation of gene-ranking reproducibility on NGS and microarray data. 相似文献12.
Tom M Conrad Andrew R Joyce M Kenyon Applebee Christian L Barrett Bin Xie Yuan Gao Bernhard Ø Palsson 《Genome biology》2009,10(10):R118-12
Background
Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. 相似文献13.
Background
To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix GeneChip system need to select both a preprocessing algorithm to obtain expression-level measurements and a way of ranking genes to obtain the most plausible candidates. We recently recommended suitable combinations of a preprocessing algorithm and gene ranking method that can be used to identify DEGs with a higher level of sensitivity and specificity. However, in addition to these recommendations, researchers also want to know which combinations enhance reproducibility. 相似文献14.
Background
T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. 相似文献15.
Background
Many common disorders have multiple genetic components which convey increased susceptibility. SNPs have been used to identify genetic components which are associated with a disease. Unfortunately, many studies using these methods suffer from low reproducibility due to lack of power. 相似文献16.
Background
Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. 相似文献17.
Background
A number of gene-profiling methodologies have been applied to microRNA research. The diversity of the platforms and analytical methods makes the comparison and integration of cross-platform microRNA profiling data challenging. In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA).Methodology/Principal Findings
The microRNA profiles of 40 human osteosarcoma xenograft samples were generated by LNA array, beads array, and TLDA. Results show that each of the three platforms perform similarly regarding intra-platform reproducibility or reproducibility of data within one platform while LNA array and TLDA had the best inter-platform reproducibility or reproducibility of data across platforms. The endogenous controls/probes contained in each platform have been observed for their stability under different treatments/environments; those included in TLDA have the best performance with minimal coefficients of variation. Importantly, we identify that the proper selection of normalization methods is critical for improving the inter-platform reproducibility, which is evidenced by the application of two non-linear normalization methods (loess and quantile) that substantially elevated the sensitivity and specificity of the statistical data assessment.Conclusions
Each platform is relatively stable in terms of its own microRNA profiling intra-reproducibility; however, the inter-platform reproducibility among different platforms is low. More microRNA specific normalization methods are in demand for cross-platform microRNA microarray data integration and comparison, which will improve the reproducibility and consistency between platforms. 相似文献18.
Niels Rahe-Meyer Christian Weilbach Matthias Karst Matthias Pawlak Aminul Ahmed Siegfried Piepenbrock Michael Winterhalter 《Biomedical engineering online》2007,6(1):1
Background
Current devices for measuring muscle contraction in vivo have limited accuracy in establishing and re-establishing the optimum muscle length. They are variable in the reproducibility to determine the muscle contraction at this length, and often do not maintain precise conditions during the examination. Consequently, for clinical testing only semi-quantitative methods have been used. 相似文献19.
20.
Julia S Bennett Keith A Jolley PFrederick Sparling Nigel J Saunders CAnthony Hart Ian M Feavers Martin CJ Maiden 《BMC biology》2007,5(1):35