This git repository consists of more detailed case reports made in conjunction with, but not part of, the article "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses", V. Nygaard, E. A. Rødland, E. Hovig, manuscript in preparation.
The target audience is the especially interested ones, and the reports are not peer-reviewed.
The format of the report is html, but the underlying r-code and text is available and rerunnable. Run knit2html or the Rstudio knitr integration on the individual .rmd files to re-produce the plots and html.
Reanalysis and alternative analysis of "Data set 2" from the original ComBat article: Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.
Reanalysis and alternative analysis of parts of Towfic et al.(2014, January). Comparing the biological impact of glatiramer acetate with the biological impact of a generic. PloS one 9(1), e83757.
Full random number re-run of the tutorial from the sva package, Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD.(2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012 Mar 15;28(6):882-3.
- helperfunctions.r ad hoc methods.
The scripts that produces the figures in "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses" are found here: https://github.com/ous-uio-bioinfo-core/batch-adjust-warning-figures.git