Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization
نویسندگان
چکیده
منابع مشابه
Physics-based analysis of Affymetrix microarray data
We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and artificial origin. Our analysis is based on a recently introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433 (2006)] which takes into accou...
متن کاملNetAffx: Affymetrix probesets and annotations
NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at ...
متن کاملQuality Assessment of the Affymetrix U133A&B Probesets by Target Sequence Mapping and Expression Data Analysis
Careful analysis of microarray probe design should be an obligatory component of MicroArray Quality Control (MACQ) project [Patterson et al., 2006; Shi et al., 2006] initiated by the FDA (USA) in order to provide quality control tools to researchers of gene expression profiles and to translate the microarray technology from bench to bedside. The identification and filtering of unreliable probes...
متن کاملADAPT: a database of affymetrix probesets and transcripts
UNLABELLED ADAPT is an online database providing comprehensive mappings between Affymetrix probes and RefSeq and Ensembl transcripts. ADAPT was designed to help interpret microarray experiments by providing a means to explore the many-to-many relationships that exist between probes, probesets, transcripts and genes. AVAILABILITY ADAPT can be queried via the web at http://bioinformatics.picr.m...
متن کاملEffects of Multiple Probesets in Affymetrix GeneChips on Identifying Differentially Expressed Genes in iPS Cells
There are multiple probesets that correspond to a gene in Affymetrix GeneChip platform. Different combination and annotation methods will lead to different results of expression when we transform the information from probesets to genes. In this work, we collected seven methods to interpret the multiple probesets for representing a gene. We compared these methods and identified their effects on ...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2014
ISSN: 1471-2164
DOI: 10.1186/1471-2164-15-s12-s8