Remove Unwanted Variation (original) (raw)

This page is being updated. (November 2018)

Articles

• Stably expressed genes in single-cell RNA-sequencing
  Julie Deeke and J. A. Gagnon-Bartsch
• scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication
  Y. Lin, S. Ghazanfar, K. Wang, J. A. Gagnon-Bartsch, K. K. Lo, X. S. Su, Z.-G. Han, J. T. Ormerod, T. P. Speed, P. Yang, and J. Y. H. Yang
• A new normalization for the Nanostring nCounter gene expression assay
  Ramyar Molania, J. A. Gagnon-Bartsch, A. Dobrovic, and T. P. Speed
• Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed
  Laurent Jacob, Johann A Gagnon-Bartsch, and Terence P Speed
• Statistical methods for handling unwanted variation in metabolomics data
  Alysha M De Livera, Marko Sysi-Aho, Laurent Jacob, Johann A Gagnon-Bartsch, Sandra Castillo, Julie A Simpson, and Terence P Speed
• Systematic noise degrades gene co-expression signals but can be corrected
  Saskia Freytag, Johann A Gagnon-Bartsch, Terence P Speed, and Melanie Bahlo
• Using control genes to correct for unwanted variation in microarray data
  Johann A Gagnon-Bartsch and Terence P Speed
• Removing unwanted variation in a differential methylation analysis of illumina humanmethylation450 array data
  Jovana Maksimovic, Johann A Gagnon-Bartsch, Terence P Speed, and Alicia Oshlack
• Removing Unwanted Variation from High Dimensional Data with Negative Controls
  J. A. Gagnon-Bartsch, L. Jacob, T. P. Speed

Software

• ruv
• RUVcorr
• RUVnormalize
• missMethyl

Datasets

• gender.sm.rda "Not preprocessed." Summarized (sm) by RMA, but without background or quantile normalization.
• gender.bgnmsm.rda "Preprocessed." Background correction (bg), quantile normalization (nm) and summarization (sm) by RMA.
• gender.bgnmsmls.rda "Fully preprocessed." Background correction (bg), quantile normalization (nm) and summarization (sm) by RMA, followed by a location-scale adjustment to account for different chip versions.
• alzheimers.sm.rda "Not preprocessed." Summarized (sm) by RMA, but without background or quantile normalization.
• alzheimers.bgnmsm.rda "Preprocessed." Background correction (bg), quantile normalization (nm) and summarization (sm) by RMA.

Lists of Stably Expressed Genes

• List of housekeeping genes from Eisenberg and Levanon (2003).
• List of single cell housekeeping genes from Lin, et al. (2017)
• Gene annotations from Deeke and Gagnon-Bartsch. The cytosolic ribosomal genes seem to be especially stable. See manuscript and supplementary information.

Additional Resources

• useR 2018 RUV tutorial on github
• Docker image on Docker Hub. Includes shiny app and tutorial.

Old

• A how-to for the old ruv_starter_analysis script.