Cargando…

Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes

While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assess...

Descripción completa

Detalles Bibliográficos
Autores principales:	Johnstone, Daniel M., Riveros, Carlos, Heidari, Moones, Graham, Ross M., Trinder, Debbie, Berretta, Regina, Olynyk, John K., Scott, Rodney J., Moscato, Pablo, Milward, Elizabeth A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2013
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003482/ https://www.ncbi.nlm.nih.gov/pubmed/27605185 http://dx.doi.org/10.3390/microarrays2020131

Ejemplares similares

Pathological relationships involving iron and myelin may constitute a shared mechanism linking various rare and common brain diseases
por: Heidari, Moones, et al.
Publicado: (2016)

Multivariate Protein Signatures of Pre-Clinical Alzheimer's Disease in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Plasma Proteome Dataset
por: Johnstone, Daniel, et al.
Publicado: (2012)

Identification of Differentially Expressed Genes through Integrated Study of Alzheimer’s Disease Affected Brain Regions
por: Puthiyedth, Nisha, et al.
Publicado: (2016)

A New Combinatorial Optimization Approach for Integrated Feature Selection Using Different Datasets: A Prostate Cancer Transcriptomic Study
por: Puthiyedth, Nisha, et al.
Publicado: (2015)

GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs
por: Arefin, Ahmed Shamsul, et al.
Publicado: (2012)

Basal-like breast cancer: molecular profiles, clinical features and survival outcomes
por: Milioli, Heloisa H., et al.
Publicado: (2017)

The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set
por: Milioli, Heloisa Helena, et al.
Publicado: (2015)

Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset
por: Milioli, Heloisa H., et al.
Publicado: (2016)

Unveiling Clusters of RNA Transcript Pairs Associated with Markers of Alzheimer’s Disease Progression
por: Arefin, Ahmed Shamsul, et al.
Publicado: (2012)

Brain iron accumulation affects myelin-related molecular systems implicated in a rare neurogenetic disease family with neuropsychiatric features
por: Heidari, M, et al.
Publicado: (2016)

Cancer Biomarker Discovery: The Entropic Hallmark
por: Berretta, Regina, et al.
Publicado: (2010)

Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing
por: Shahandeh, Al, et al.
Publicado: (2016)

Importance of randomization in microarray experimental designs with Illumina platforms
por: Verdugo, Ricardo A., et al.
Publicado: (2009)

QAPgrid: A Two Level QAP-Based Approach for Large-Scale Data Analysis and Visualization
por: Inostroza-Ponta, Mario, et al.
Publicado: (2011)

Model-based variance-stabilizing transformation for Illumina microarray data
por: Lin, Simon M., et al.
Publicado: (2008)

illuminaio: An open source IDAT parsing tool for Illumina microarrays
por: Smith, Mike L, et al.
Publicado: (2013)

Gene co-expression networks shed light into diseases of brain iron accumulation
por: Bettencourt, Conceição, et al.
Publicado: (2016)

Heterogeneous Ensemble Combination Search Using Genetic Algorithm for Class Imbalanced Data Classification
por: Haque, Mohammad Nazmul, et al.
Publicado: (2016)

A Novel Clustering Methodology Based on Modularity Optimisation for Detecting Authorship Affinities in Shakespearean Era Plays
por: Naeni, Leila M., et al.
Publicado: (2016)

Evaluation of microarray data normalization procedures using spike-in experiments
por: Rydén, Patrik, et al.
Publicado: (2006)

Image Analysis and Data Normalization Procedures are Crucial for Microarray Analyses
por: Kadanga, Ali Kpatcha, et al.
Publicado: (2008)

Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the Changes of Hippocampus' Gene Expression Profiles in Alzheimer's Disease
por: Gómez Ravetti, Martín, et al.
Publicado: (2010)

Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays
por: Seiser, Eric L, et al.
Publicado: (2015)

Differences in Abundances of Cell-Signalling Proteins in Blood Reveal Novel Biomarkers for Early Detection Of Clinical Alzheimer's Disease
por: Rocha de Paula, Mateus, et al.
Publicado: (2011)

A prospective cohort examination of haematological parameters in relation to cancer death and incidence: the Busselton Health Study
por: Adris, Niwansa, et al.
Publicado: (2018)

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays
por: Du, Pan, et al.
Publicado: (2007)

CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays
por: Alonso, Arnald, et al.
Publicado: (2010)

Mouse strain specific gene expression differences for illumina microarray expression profiling in embryos
por: Kraus, Petra, et al.
Publicado: (2012)

Alzheimer’s disease patient groups derived from a multivariate analysis of cognitive test outcomes in the Coalition Against Major Diseases dataset
por: Tishchenko, Inna, et al.
Publicado: (2016)

A new model calling procedure for Illumina BeadArray data
por: Li, Gengxin
Publicado: (2016)

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments
por: Kitchen, Robert R, et al.
Publicado: (2011)

Illumina next generation sequencing data and expression microarrays data from retinoblastoma and medulloblastoma tissues
por: García-Chequer, A.J., et al.
Publicado: (2016)

Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays
por: Zhang, Wei, et al.
Publicado: (2023)

Illumina WG-6 BeadChip strips should be normalized separately
por: Shi, Wei, et al.
Publicado: (2009)

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
por: Fortin, Jean-Philippe, et al.
Publicado: (2017)

Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray
por: Chen, Yi-an, et al.
Publicado: (2013)

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
por: Pidsley, Ruth, et al.
Publicado: (2016)

Battle of epigenetic proportions: comparing Illumina’s EPIC methylation microarrays and TruSeq targeted bisulfite sequencing
por: Heiss, Jonathan A., et al.
Publicado: (2019)

Supervised normalization of microarrays
por: Mecham, Brigham H., et al.
Publicado: (2010)

Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers
por: Tishchenko, Inna, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_q4rq4teraouikn0gs757bfmuts