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A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
MOTIVATION When running experiments that involve multiple high density oligonucleotide arrays, it is important to remove sources of variation between arrays of non-biological origin. Normalization is… Expand
Summaries of Affymetrix GeneChip probe level data.
- R. Irizarry, B. Bolstad, F. Collin, L. Cope, B. Hobbs, T. Speed
- Medicine, Biology
- Nucleic acids research
- 15 February 2003
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are… Expand
affy - analysis of Affymetrix GeneChip data at the probe level
MOTIVATION The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely… Expand
Frozen robust multiarray analysis (fRMA).
Robust multiarray analysis (RMA) is the most widely used preprocessing algorithm for Affymetrix and Nimblegen gene expression microarrays. RMA performs background correction, normalization, and… Expand
Spotted long oligonucleotide arrays for human gene expression analysis.
- Andrea J Barczak, Madeleine W Rodriguez, +5 authors D. Erle
- Biology, Medicine
- Genome research
- 1 July 2003
DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted… Expand
Quality Assessment of Affymetrix GeneChip Data
This chapter covers quality assessment for Affymetrix GeneChip data. The focus is on procedures available from the affy and affy-PLM packages. Initially some exploratory plots provided by the affy… Expand
Quality Assessment for Short Oligonucleotide Microarray Data
- J. Brettschneider, F. Collin, B. Bolstad, T. Speed
- Computer Science, Mathematics
- 30 September 2007
Quality of microarray gene expression data has emerged as a new research topic. As in other areas, microarray quality is assessed by comparing suitable numerical summaries across microarrays, so that… Expand
Iodixanol in Femoral Arteriography
Two contrast media, iodixanol (Visipaque, Nycomed) 270 mg I/ml and iohexol (Omnipaque, Nycomed) 300 mg I/ml, were compared in femoral arteriography, in 147 patients. Both contrast media were… Expand
Preprocessing High-density Oligonucleotide Arrays
High-density oligonucleotide expression arrays are a widely used microarray platform. Affymetrix GeneChip arrays dominate this market. An important distinction between the GeneChip and other… Expand
FROZEN ROBUST MULTI-ARRAY ANALYSIS (fRMA)
Robust Multi-array Analysis (RMA) is the most widely used preprocessing algorithm for Affymetrix and Nimblegen gene-expression microarrays. RMA performs background correction, normalization, and… Expand