Additional file 7: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Additional file 4 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S4. Consistency of estimated gene expression from various methods for the paired-end sample U...

Assessing and accounting for correlation in RNA-seq data analysis

Liu, Meiling

January 2019

RNA-sequencing (RNA-seq) technology is a high-throughput next-generation sequencing procedure. It al...

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated transcripts.

Lucy Mackenzie-Impoinvil (6278108)
Gareth D. Weedall (215713)
Juan C. Lol (6278111)
Jesús Pinto (6278114)
Lucrecia Vizcaino (6278117)
Nicole Dzuris (6278120)
Jacob Riveron (3440567)
Norma Padilla (44896)
Charles Wondji (3419594)
Audrey Lenhart (354002)

January 2019

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated tra...

Additional file 8: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Spearmanâs correlation to RT-qPCR data of 30 genes. Correlation coefficients (x-axis) of 30 genes ...

Additional file 1: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Impact of gene length correction on correlation. Simulated expression data of 10 genes in 2 samples....

Additional file 4: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Details on the settings for the STAR algorithm and R commands to obtain normalized data. (DOCX 13 kb

Additional file 9: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Library size and PCA plots by RIN. A shows the library size (log10) in samples with low RIN values (...

Additional file 2: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Correlation RIN BioAnalyzer vs MultiNA. RIN values as measured by the Bioanalyzer (Agilent) were com...

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Smid, Marcel
Coebergh van den Braak, Robert
Werken, Harmen
Riet, Job
Galen, Anne
Weerd, Vanja
van der Vlugt-Daane, M. (Michelle)
Bril, S.I. (Sandra I.)
Lalmahomed, Zarina
Kloosterman, Wigard
Wilting, Saskia
Foekens, John
IJzermans, Jan
Martens, John
Sieuwerts, Anieta

June 2018

textabstractBackground: Current normalization methods for RNA-sequencing data allow either for inter...

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid
Robert R. J. Coebergh van den Braak
Harmen J. G. van de Werken
Job van Riet
Anne van Galen
Vanja de Weerd
Michelle van der Vlugt-Daane
Sandra I. Bril
Zarina S. Lalmahomed
Wigard P. Kloosterman
Saskia M. Wilting
John A. Foekens
Jan N. M. IJzermans
on behalf of the MATCH study group
John W. M. Martens
Anieta M. Sieuwerts

June 2018

Abstract Background Current normalization methods for RNA-sequencing data allow either for intersamp...

Additional file 4 of Limitations of alignment-free tools in total RNA-seq quantification

Douglas C. Wu (674101)
Jun Yao (9646)
Kevin S. Ho (5480165)
Alan M. Lambowitz (9648)
Claus O. Wilke (188638)

July 2018

Pearson’s correlation coefficients for pairwise pipeline comparisons in gene quantifications. For ev...

Additional file 5 of Limitations of alignment-free tools in total RNA-seq quantification

Douglas C. Wu (674101)
Jun Yao (9646)
Kevin S. Ho (5480165)
Alan M. Lambowitz (9648)
Claus O. Wilke (188638)

July 2018

Impact of gene lengths and expression levels on gene quantification correlations among pipelines. (a...

Additional file 1 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S1. Comparison of expression estimation accuracy at gene level for the MAQC data. Pearson cor...

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Smid, M. (Marcel)
Coebergh van den Braak, R.R.J. (Robert)
Werken, H.J.G. (Harmen) van de
Riet, J. (Job) van
Galen, A. (Anne) van
Weerd, V. (Vanja) de
van der Vlugt-Daane, M. (Michelle)
Bril, S.I. (Sandra I.)
Lalmahomed, Z.S. (Zarina)
Kloosterman, W.P. (Wigard)
Wilting, S.M. (Saskia)
Foekens, J.A. (John)
IJzermans, J.N.M. (Jan)
Martens, J.W.M. (John)
Sieuwerts, A.M. (Anieta)

June 2018

Background: Current normalization methods for RNA-sequencing data allow either for intersample compa...

Additional file 3 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S3. Consistency of estimated gene expression from various methods for the single-end sample U...

Additional file 4 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S4. Consistency of estimated gene expression from various methods for the paired-end sample U...

Assessing and accounting for correlation in RNA-seq data analysis

Liu, Meiling

January 2019

RNA-sequencing (RNA-seq) technology is a high-throughput next-generation sequencing procedure. It al...

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated transcripts.

Lucy Mackenzie-Impoinvil (6278108)
Gareth D. Weedall (215713)
Juan C. Lol (6278111)
Jesús Pinto (6278114)
Lucrecia Vizcaino (6278117)
Nicole Dzuris (6278120)
Jacob Riveron (3440567)
Norma Padilla (44896)
Charles Wondji (3419594)
Audrey Lenhart (354002)

January 2019

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated tra...

Additional file 8: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Spearmanâs correlation to RT-qPCR data of 30 genes. Correlation coefficients (x-axis) of 30 genes ...

Additional file 1: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Impact of gene length correction on correlation. Simulated expression data of 10 genes in 2 samples....

Additional file 4: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Details on the settings for the STAR algorithm and R commands to obtain normalized data. (DOCX 13 kb

Additional file 9: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Library size and PCA plots by RIN. A shows the library size (log10) in samples with low RIN values (...

Additional file 2: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid (54590)
Robert Coebergh van den Braak (5437478)
Harmen van de Werken (5437481)
Job van Riet (5437487)
Anne van Galen (3525365)
Vanja de Weerd (1354092)
Michelle van der Vlugt-Daane (3072198)
Sandra Bril (5437472)
Zarina Lalmahomed (5437475)
Wigard Kloosterman (3698350)
Saskia Wilting (5351063)
John Foekens (3521840)
Jan IJzermans (5437484)
John Martens (3502718)
Anieta Sieuwerts (3525362)

June 2018

Correlation RIN BioAnalyzer vs MultiNA. RIN values as measured by the Bioanalyzer (Agilent) were com...

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Smid, Marcel
Coebergh van den Braak, Robert
Werken, Harmen
Riet, Job
Galen, Anne
Weerd, Vanja
van der Vlugt-Daane, M. (Michelle)
Bril, S.I. (Sandra I.)
Lalmahomed, Zarina
Kloosterman, Wigard
Wilting, Saskia
Foekens, John
IJzermans, Jan
Martens, John
Sieuwerts, Anieta

June 2018

textabstractBackground: Current normalization methods for RNA-sequencing data allow either for inter...

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Marcel Smid
Robert R. J. Coebergh van den Braak
Harmen J. G. van de Werken
Job van Riet
Anne van Galen
Vanja de Weerd
Michelle van der Vlugt-Daane
Sandra I. Bril
Zarina S. Lalmahomed
Wigard P. Kloosterman
Saskia M. Wilting
John A. Foekens
Jan N. M. IJzermans
on behalf of the MATCH study group
John W. M. Martens
Anieta M. Sieuwerts

June 2018

Abstract Background Current normalization methods for RNA-sequencing data allow either for intersamp...

Additional file 4 of Limitations of alignment-free tools in total RNA-seq quantification

Douglas C. Wu (674101)
Jun Yao (9646)
Kevin S. Ho (5480165)
Alan M. Lambowitz (9648)
Claus O. Wilke (188638)

July 2018

Pearson’s correlation coefficients for pairwise pipeline comparisons in gene quantifications. For ev...

Additional file 5 of Limitations of alignment-free tools in total RNA-seq quantification

Douglas C. Wu (674101)
Jun Yao (9646)
Kevin S. Ho (5480165)
Alan M. Lambowitz (9648)
Claus O. Wilke (188638)

July 2018

Impact of gene lengths and expression levels on gene quantification correlations among pipelines. (a...

Additional file 1 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S1. Comparison of expression estimation accuracy at gene level for the MAQC data. Pearson cor...

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Smid, M. (Marcel)
Coebergh van den Braak, R.R.J. (Robert)
Werken, H.J.G. (Harmen) van de
Riet, J. (Job) van
Galen, A. (Anne) van
Weerd, V. (Vanja) de
van der Vlugt-Daane, M. (Michelle)
Bril, S.I. (Sandra I.)
Lalmahomed, Z.S. (Zarina)
Kloosterman, W.P. (Wigard)
Wilting, S.M. (Saskia)
Foekens, J.A. (John)
IJzermans, J.N.M. (Jan)
Martens, J.W.M. (John)
Sieuwerts, A.M. (Anieta)

June 2018

Background: Current normalization methods for RNA-sequencing data allow either for intersample compa...

Additional file 3 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S3. Consistency of estimated gene expression from various methods for the single-end sample U...

Additional file 4 of Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Xuejun Liu (427262)
Xinxin Shi (3510374)
Chunlin Chen (1511164)
Li Zhang (8200)

October 2015

Figure S4. Consistency of estimated gene expression from various methods for the paired-end sample U...

Assessing and accounting for correlation in RNA-seq data analysis

Liu, Meiling

January 2019

RNA-sequencing (RNA-seq) technology is a high-throughput next-generation sequencing procedure. It al...

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated transcripts.

Lucy Mackenzie-Impoinvil (6278108)
Gareth D. Weedall (215713)
Juan C. Lol (6278111)
Jesús Pinto (6278114)
Lucrecia Vizcaino (6278117)
Nicole Dzuris (6278120)
Jacob Riveron (3440567)
Norma Padilla (44896)
Charles Wondji (3419594)
Audrey Lenhart (354002)

January 2019

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated tra...

Additional file 7: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Abstract

Extracted data

Additional file 7: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Abstract

Extracted data

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