User profiles for J. A. Gagnon-Bartsch
Johann Gagnon-BartschAssociate Professor of Statistics, University of Michigan Verified email at umich.edu Cited by 2035 |
Using control genes to correct for unwanted variation in microarray data
JA Gagnon-Bartsch, TP Speed - Biostatistics, 2012 - academic.oup.com
Microarray expression studies suffer from the problem of batch effects and other unwanted
variation. Many methods have been proposed to adjust microarray data to mitigate the …
variation. Many methods have been proposed to adjust microarray data to mitigate the …
Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas
Objective Differences in gastric cancer (GC) clinical outcomes between patients in Asian
and non-Asian countries has been historically attributed to variability in clinical management. …
and non-Asian countries has been historically attributed to variability in clinical management. …
Statistical methods for handling unwanted variation in metabolomics data
Metabolomics experiments are inevitably subject to a component of unwanted variation, due
to factors such as batch effects, long runs of samples, and confounding biological variation. …
to factors such as batch effects, long runs of samples, and confounding biological variation. …
scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets
…, KYX Wang, JA Gagnon-Bartsch… - Proceedings of the …, 2019 - National Acad Sciences
Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq)
data promises further biological insights that cannot be uncovered with individual datasets. …
data promises further biological insights that cannot be uncovered with individual datasets. …
[PDF][PDF] Removing unwanted variation from high dimensional data with negative controls
… upon the work of Gagnon-Bartsch and Speed (2012). GagnonBartsch and Speed (2012) …
in this paper are not identical to those in Gagnon-Bartsch and Speed (2012). TCGA has …
in this paper are not identical to those in Gagnon-Bartsch and Speed (2012). TCGA has …
Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed
When dealing with large scale gene expression studies, observations are commonly
contaminated by sources of unwanted variation such as platforms or batches. Not taking this …
contaminated by sources of unwanted variation such as platforms or batches. Not taking this …
A new normalization for Nanostring nCounter gene expression data
The Nanostring nCounter gene expression assay uses molecular barcodes and single
molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These …
molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These …
Dtangle: accurate and robust cell type deconvolution
…, S Freytag, M Bahlo, JA Gagnon-Bartsch - Bioinformatics, 2019 - academic.oup.com
… Johann A Gagnon-Bartsch Johann A Gagnon-Bartsch … Gregory J Hunt, Saskia Freytag,
Melanie Bahlo, Johann A Gagnon-Bartsch, dtangle: accurate and robust cell type deconvolution, …
Melanie Bahlo, Johann A Gagnon-Bartsch, dtangle: accurate and robust cell type deconvolution, …
Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data
J Maksimovic, JA Gagnon-Bartsch… - Nucleic acids …, 2015 - academic.oup.com
… is performing; examples of some useful approaches can be found in this study and are
also discussed in detail in Gagnon-Bartsch and Speed (22) and Gagnon-Bartsch et al. (23). …
also discussed in detail in Gagnon-Bartsch and Speed (22) and Gagnon-Bartsch et al. (23). …
[HTML][HTML] Removing unwanted variation from large-scale RNA sequencing data with PRPS
Accurate identification and effective removal of unwanted variation is essential to derive
meaningful biological results from RNA sequencing (RNA-seq) data, especially when the data …
meaningful biological results from RNA sequencing (RNA-seq) data, especially when the data …