Hands-On: A Framework for Oligonucleotide Microarrays Preprocessing
نویسندگان
چکیده
This document provides examples on the usage of the oligo package. The datasets used here can be downloaded by the user, who is expected to have the CEL and XYS files in the following directory structure: Directory Name Object Name Description expressionData affyExpressionFS Latin Square Affymetrix U95A exonData affyExonFS Exon Sample Dataset Human snpData affySnpFS HapMap samples on XBA Array tilingData nimbleTilingFS Sample ChIP-chip dataset Table 1: Directory structure used in this document to store CEL and XYS files. http://www.affymetrix.com/support/technical/sample_data/datasets.affx http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx http://hapmap.ncbi.nlm.nih.gov/downloads/raw_data/affy100k/ Data available upon request and provided by NimbleGen
منابع مشابه
An Efficient Covalent Coating on Glass Slides for Preparation of Optical Oligonucleotide Microarrays
Objective(s): Microarrays are potential analyzing tools for genomics and proteomics researches, which is in needed of suitable substrate for coating and also hybridization of biomolecules. Materials and Methods: In this research, a thin film of oxidized agarose was prepared on the glass slides which previously coated with poly-L-lysine (PLL). Some of the aldehyde groups of the activated aga...
متن کاملA computational framework for optimal masking in the synthesis of oligonucleotide microarrays.
High-throughput genomic technologies are revolutionizing modern biology. In particular, DNA microarrays have become one of the most powerful tools for profiling global mRNA expression in different tissues and environmental conditions, and for detecting single nucleotide polymorphisms. The broad applicability of gene expression profiling to the biological and medical realms has generated expandi...
متن کاملExploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists, and clinicians. These data manipulations, referred to as preprocessing, can influence the quality of the ultimate measurements. In the last few years, the high-throughput measurement of gene expression is the most popular applicat...
متن کاملTowards Quality Control for DNA Microarrays
We present a framework for detecting probes in oligonucleotide microarrays that may add significant error to measurements in hybridization experiments. Four types of so-called degenerate probe behavior are considered: secondary structure formation, self-dimerization, cross-hybridization, and dimerization. The framework uses a well-established model for computing the free energy of nucleic acid ...
متن کاملProfound Transcriptomic Differences Found between Sperm Samples from Sperm Donors vs. Patients Undergoing Assisted Reproduction Techniques Tends to Disappear after Swim-up Sperm Preparation Technique
Background Although spermatozoa delivers its RNA to oocytes at fertilization, its biological role is not well characterized. Our purpose was to identify the genes differentially and exclusively expressed in sperm samples both before and after the swim-up process in control donors and infertile males with the purpose to identify their functional significance in male fertility. MaterialsAndMethod...
متن کامل