A comprehensive re-analysis of the Golden Spike data: towards a benchmark for differential expression methods (Q31150638)

14 November 2017

A comprehensive re-analysis of the Golden Spike data: towards a benchmark for differential expression methods (English)

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14 November 2017

Richard D Pearson

1

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14 November 2017

26 March 2008

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14 November 2017

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14 November 2017

9

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14 November 2017

164

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Creative Commons Attribution 2.0 Generic

14 November 2017

start time

26 March 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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April 2022 Public Data File from Crossref

describes a project that uses

affy

object named as

affy

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

limma

object named as

limma

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-9-164

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cites work

Estimation and correction of non-specific binding in a large-scale spike-in experiment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Towards the uniform distribution of null P values on Affymetrix microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

A new summarization method for Affymetrix probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Microarray data analysis: from disarray to consolidation and consensus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

ROCR: visualizing classifier performance in R

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Significance analysis of microarrays applied to the ionizing radiation response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

A distribution free summarization method for Affymetrix GeneChip(R) arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Feature-level exploration of a published Affymetrix GeneChip control dataset

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

Probe-level measurement error improves accuracy in detecting differential gene expression.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

A reanalysis of a published Affymetrix GeneChip control dataset

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

A benchmark for Affymetrix GeneChip expression measures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2324099

31 October 2018

Identifiers

DOI

10.1186/1471-2105-9-164

1 reference

14 November 2017

journals/bmcbi/Pearson08

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

14 November 2017

1 reference

PMCID

2324099