We have performed a series of calibration and comparative experiments to address several important issues in data analysis and study design of microarray experiments. As the cdna microarray era progressed, it was noted that the reference design was not the optimal experimental design for all experiments. The multistep, dataintensive nature of this technology has created an unprecedented informatics and analytical challenge. In this section, some of the design issues that arise with the twocolor cdna or long oligonucleotide microarray experiments are discussed. We overview various issues that affect the design of i experiments for cdna spotted microarrays and ii high density oligonucleotide gene expression experiments. Reverse fluor experiments allocation of samples to cdna array experiments kerr and churchill, biostatistics, 2001 dobbin and simon, bioinformatics, in press.
Sample size determination in microarray experiments for. Experimental designs for 2colour cdna microarray experiments. Sep 03, 2015 biological background of microarray experiments. Microarray experiments involve huge data handling and extensive procedures. Assessing gene significance from cdna microarray expression data via mixed models. Using lower amounts of rna for ge microarray experiments. By representing the experiment as a graph, where the timepoints are nodes and the arrays are edges, we demonstrate how the time contrasts between any two timepoints can be. Design and validation issues in rnaseq experiments. Systematic variations can occur at various steps of a cdna microarray experiment and affect the measurement of gene expression levels. Considerations for experimental design article pdf available in south african journal of science 1017.
As with all largescale experiments, they can be costly in terms of equipment, consumables and time. Microarray experiments and factors which affect their. Experimental design and analysis of antibody microarrays. With more than two conditions, analysis of variance anova can be used, and the mixed anova model is a general and powerful. For a given question, there wont be one right design.
Statistical issues in the design and analysis of gene. Mar 17, 2003 extracting biological information from microarray data requires appropriate statistical methods. Extracting biological information from microarray data requires appropriate statistical methods. Statistical issues in the analysis of microarray data. Topics on statistical design and analysis of cdna microarray. We would like to show you a description here but the site wont allow us. Many of these objectives fall into the following categories 59. Design considerations sample selection sample size planning controls sources of variabilitylevels of replication for cdna2color spotted arrays. In the next section, we discuss design issues to be considered for microarray animal experiments. Microarrays a microarray is a pattern of ssdna probes which are immobilized on a surface called a chip or a slide.
The probe sequences are designed and placed on an array in a regular pattern of spots. Microarray experiments and factors which affect their reliability. It is important to understand the crucial steps that can affect the outcome of the analysis. Practical microarray analysis experimental design heidelberg, march 2003 14 sample size calculation for a microarray experiment iv in order to complete the sample size calculation for a microarray experiment, information on. Scientists use dna microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. In this paper, several aspects of study design are discussed, including the number of animals that need to be studied to ensure sufficiently powered studies, usefulness of replication and pooling, and. Jean yee hwa yang is an australian statistician known for her work on variance reduction for microarrays, and for inferring proteins from mass spectrometry data. Reassessing design and analysis of twocolour microarray. Full text views reflects the number of pdf downloads, pdfs sent.
Sample size determination in microarray experiments for class. Factorial and time course designs for cdna microarray experiments. Oct 01, 2006 microarray experiments have been used recently in genetical genomics studies, as an additional tool to understand the genetic mechanisms governing variation in complex traits, such as for estimating heritabilities of mrna transcript abundances, for mapping expression quantitative trait loci, and for inferring regulatory networks controlling gene expression. The design of scientific experiments is an art of balancing considerations. Fundamentals of experimental design for cdna microarrays. Design issues in toxicogenomics using dna microarray. With a fixed number of specimens, reference design is. A random variance model for detection of differential gene detection in small microarray experiments. In a cdna microarray, each gene of interest is represented by a long dna fragment 2002400 bp typically generated by polymerase chain reaction pcr and spotted on glass slides using robotics i. A random variance model for detection of differential gene detection in small microarray. One type consists of several interwoven loops, and the other type combines reference and loop designs. Topics on statistical design and analysis of cdna microarray experiment ximin zhu a dissertation submitted to the university of glasgow for the degree of. Practical microarray analysis experimental design heidelberg, october 2003 2 experiments scientists deal mostly with experiments of the following form.
The microarray experiment is a multistage process in which the accuracy of each individual step may influence the gene expression. Anyone collecting and analyzing data, be it in the lab, the field or the production plant, can benefit from knowledge about experimental design. A number of alternative conditions treatments one of which is applied to each experimental unit an observation or several observations then being made on each unit. Design issues have also been discussed by other researchers, including jin et al. Design of microarray experiments bioconductor home.
In this article we propose two practical types of designs for large timecourse, dualchannel microarray experiments. The issues associated with the microarray experiments therefore requires careful handling to get the best quality of data. Factorial and time course designs for cdna microarray. Synthesizing data for research questions 31 two aliquots. A dna microarray also commonly known as dna chip or biochip is a collection of microscopic dna spots attached to a solid surface. Microarray experiments are used to quantify and compare gene expression on. Design issues in toxicogenomics using dna microarray experiment design issues in toxicogenomics using dna microarray experiment lee, kyoungmu. For class discovery, a reference design is preferable because of large gains in cluster performance. A microarray is a powerful tool for surveying the expression levels of many thousands of. Due to the complex nature and sheer amount of data produced from microarray experiments, biologists have sought the collab. Microarray analysis the basics thomas girke december 9, 2011 microarray analysis slide 142. Yang is a professor in the school of mathematics and statistics at the university of sydney. Design issues for cdna microarray experiments nature. The discussion focuses on twocolor spotted cdna microarrays, but many of the same issues apply to singlecolor geneexpression assays as well.
Optimal factorial designs for cdna microarray experiments. Scientists use dna microarrays to measure the expression levels of. One type consists of several interwoven loops, and the other type. A typical microarray experiment is one who looks for genes di erentially expressed between two or more conditions. Experimental design issues in microarray data analysis. Dna microarray technologies, such as cdna and oligonucleotide microarrays, promise to rev olutionize biological research and further our understanding of biological processes. Minimum information about a microarray experiment an. Statistical tests for differential expression in cdna. Experimental issues in microarrays biotech articles.
Besides processing date, technician and reagent batch, which are commonly known to investigators, there are some recognized technical effects specific to the rnaseq procedures. Designing experiments with radiolabelled cdna arrays on nylon membranes or for. Wolfinger rd, gibson g, wolfinger ed, bennett l, hamadeh h, bushel p, afshari c, paules rs. Microarray technology is a powerful approach for genomics research. Design of large timecourse microarray experiments with two. Designing microarray experiments the appropriate design of a microarray experiment must consider design of the array allocation of mrna samples to the slides both aspects are influenced by different sets of parameters, ultimately the decisions must be guided by the questions that have to be answered. Statistical design and the analysis of gene expression. Microarray analysis data analysis slide 2742 performance comparison of a y methods qin et al. Next, we proceed to describe the microarray experimental procedure in section 3 for cdna microarrays schena et al. Appropriate statistical design and analysis of gene expression microarray studies is critical in order to draw valid and useful conclusions from expression profiling studies of animal models. Madan babu abstract this chapter aims to provide an introduction to the analysis of gene expression data obtained using microarray experiments. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. Design of microarray experiments for genetical genomics.
Design issues for cdna microarray experiments yee hwa yang and terry speed microarray experiments are used to quantify and compare gene expression on a large scale. The authors apply classical statistical experimental design to cdna microarray experiments and keep cy3 and cy5 spot intensities separate in the analysis. Design issues in toxiconomics using dna microarry experiment. As in microarray studies, rnaseq experiments can be affected by the variability coming from nuisance factors, often called technical effects in the rnaseq literature. Experimental designs for 2colour cdna microarray experiments namky nguyen1,z and e. Sep 01, 2005 design issues in toxicogenomics using dna microarray experiment in omics study, microarray is the most popular approach. Linear models and empirical bayes methods for assessing di. Careful experimental design and initial calibration experiments can minimize those.
Design issues in toxicogenomics using dna microarray experiment. One of each is labeled with each dye, and the samples are then hybridized with the sample. The design recommendations may differ depending on the scientific aims and array platform. Practical microarray analysis experimental design heidelberg, october 2003 4 main requirements for experiments once the conditions treatments, experimental units, and the nature of the observations.
The simplest statistical method for detecting differential expression is the t test, which can. Request pdf design issues in toxiconomics using dna microarry experiment the methods of toxicogenomics might be classified into omics study e. Minimum information about a microarray experiment miame is a proposal describing the fundamental information that is required to allow for the interpretation and independent verification of microarray data, and it provides a set of standards for recording and reporting microarray data. In this section, some of the design issues that arise with the twocolor cdna or long. The microarray experiment is a multistage process in which the accuracy of each individual step may influence the gene expression estimates. Practical microarray analysis experimental design heidelberg, september 2002 4 experimental design issues for microarrys design of the array itself. Precise understanding of each step is very important not only for the experimenter but also for the person performing data preprocessing. Standardization of protocols in cdna microarray analysis. Williams2,y 1school of mathematics, statistics and computer science, university of new england, armidale, nsw 2351, australia 2statistical consulting unit, the australian national university, canberra, australia summary. Designing microarray experiments the appropriate design of a microarray experiment must consider design of the array allocation of mrna samples to the slides both aspects are influenced by different.
Topics on statistical design and analysis of cdna microarray experiment ximin zhu a dissertation submitted to the university of glasgow for the degree of doctor of philosophy department of statistics may 2009 c ximin zhu, may 2009. Minimum information about a microarray experiment miame is a proposal describing the fundamental information that is required to allow for. Statistical analysis of microarray data richard simon lisa m. With a fixed number of arrays, block design is more efficient than loop or reference design, but block design precludes clustering. At the onset of the cdna microarray era, the reference design was used in which samples of interest were labeled with one fluorescent dye e. Design and analysis of comparative microarray experiments. Topics on statistical design and analysis of cdna microarray experiment. In cdna microarray experiments, a pair of images is produced and processed by different kinds of software for image analysis to r,g fluorescence intensity pairs for each gene on each array where r red for cy5 and g green for cy3. Jun 15, 2001 we have performed a series of calibration and comparative experiments to address several important issues in data analysis and study design of microarray experiments. In each calibration experiment we purified total rna from escherichia coli cells and divided the sample into two aliquots for labeling by cy3 and cy5.
In this paper we refer to two widely used array platforms duallabel spotted cdna arrays and singlelabel affymetrixstyle oligonucleotide arrays. Design of large timecourse microarray experiments with. Microarrays platforms can be divided into three categories. Aug 22, 2012 in this article we propose two practical types of designs for large timecourse, dualchannel microarray experiments. We relate certain features of microarrays to other kinds of experimental data and argue that classical statistical techniques are appropriate and useful. Microarray experiments have been used recently in genetical genomics studies, as an additional tool to understand the genetic mechanisms governing variation in complex traits, such as.
1478 1086 928 1001 640 1026 1281 427 1476 1298 1087 10 1415 1520 818 23 455 96 1537 500 93 1550 282 782 959 1509 723 656 60 448 208 564 419 175 1494 1413 1018