Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
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...Gut microbiota associated with colorectal cancer were recently shown to have an increase in genes associated with TMA lyase and protein catabolism, while microbe carbohydrate degradation pathways were depleted [156,157]....
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"Meta-analysis of fecal metagenomes ..." refers methods in this paper
...To adjust for multiple hypothesis testing, P-values were adjusted using the 823 false-discovery rate (FDR) method [70]....
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"Meta-analysis of fecal metagenomes ..." refers methods in this paper
...For each split, a L1-regularized 875 (LASSO) logistic regression model [68] was trained on the training set, which was then used to predict 876 the test set....
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...LASSO models were then built on log10-transformed abundances (pseudocount of 10 × 10−9, centered and scaled) of the sets of the 100 top genes returned by mRMR....
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...Instead, least absolute shrinkage and selection operator (LASSO) logistic regression classifiers were employed to select predictive microbial features and eliminated uninformative ones (see Methods)....
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...To ascertain the predictive power of a classifier based on the IGC gene abundances30, we applied a series of filters to the abundance tables to reduce the number of genes that would be the input of LASSO modeling....
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...This importantly 800 also pertained to feature selection, which was either done via the LASSO [68] or by nested cross801 validation procedures to avoid overoptimistic performance assessment [69] (see below for details)....
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