(Q33433707)

26 July 2017

title

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity (English)

1 reference

26 July 2017

1 reference

Koji Kadota

1

0 references

author name string

Yuji Nakai

series ordinal

2

1 reference

26 July 2017

Kentaro Shimizu

series ordinal

3

1 reference

26 July 2017

language of work or name

English

0 references

publication date

22 April 2009

1 reference

Algorithms for Molecular Biology

26 July 2017

published in

1 reference

26 July 2017

volume

4

1 reference

26 July 2017

issue

1

0 references

page(s)

7

1 reference

Creative Commons Attribution 2.0 Generic

26 July 2017

copyright license

start time

22 April 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

describes a project that uses

limma

object named as

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/2679019

based on heuristic

inferred from PubMed Central ID database lookup

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

affy

object named as

affy

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/1748-7188-4-7

0 references

cites work

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

"Hook"-calibration of GeneChip-microarrays: theory and algorithm

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

A weighted average difference method for detecting differentially expressed genes from microarray 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=2679019

A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression 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=2679019

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

Up-regulation of genes related to the ubiquitin-proteasome system in the brown adipose tissue of 24-h-fasted rats

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP 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=2679019

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes 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=2679019

NCBI GEO: mining tens of millions of expression profiles--database and tools update

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

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=2679019

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=2679019

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=2679019

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=2679019

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=2679019

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=2679019

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=2679019

Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated 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=2679019

affy--analysis of Affymetrix GeneChip data at the probe level

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

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=2679019

Variance stabilization applied to microarray data calibration and to the quantification of differential 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=2679019

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=2679019

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=2679019

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=2679019

Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

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=2679019

Comparison of 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=2679019

Robust estimators for expression analysis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679019

Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19386098

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1748-7188-4-7

1 reference

journals/almob/KadotaNS09

26 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1 reference

https://scigraph.springernature.com/pub.10.1186/1748-7188-4-7

9 September 2019

1 reference

26 July 2017

1 reference