Teng Fei

icon indicating a website link https://www.mskcc.org/profile/teng-fei

icon company MSKCC icon location Biostatistician at MSKCC. Latent class analysis; microbiome data; competing risks; longitudinal data; batch effect adjustment

Results 5 comments of Teng Fei

How to obtain a corrected count/expression matrix?

Thank you for your inquiries. Indeed, the negative values in the output matrix is a common issue for batch effect correction tools. To be frank, when we test our method...

I can not reproduce your example code

It seems that the latest version of package scater renamed the normalise function as logNormCounts. You may try logNormCounts(sim.groups) instead.

I can not reproduce your example code

You need to install Rtools to compile this package: https://cran.r-project.org/bin/windows/Rtools/.

Installation error

Thank you for letting me know. Maybe the following post can provide some suggestion https://daijiang.name/en/2017/06/21/fopenmp-option-of-clang-error/. I built the package under windows environment and I did not encounter issues on installation...

Unexpected outputs using `car::Anova()` on a `tidycrr` object?

@ddsjoberg I think the test used should be `aod::wald.test()`. I never used `car::Anova()` for a `crr` or `tidycrr` object and I am not sure how it works.