The bioBakery help forum

Feature request: automatic independent filtering of features like DESeq2

Hi,

Thanks for developing the MaAsLin2 that enables incorporating random effects in the models. To reduce the number of multiple testing, MaAsLin2 allows filtering uninformative features that have low counts and/or low prevalence. However, the filtering thresholds are somewhat arbitrary, often determined based on users’ knowledge or preference. The differential gene expression analysis software, DESeq2, has a function for automatic independent filtering of features that maximizes the number of genes found at a user-specified target FDR. Is it possible to implement a similar function in MaAsLin2?

Best,
Yanxian

Hi -
Thanks for the suggestion - this is a great idea. I’ve talked to the developer and we plan to incorporate this for the next release of Bioconductor. We’ll make sure to credit you for suggesting this feature.
Best,
Siyuan

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