Additional file 1 of Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

Additional file 1: Gene count estimates. Model (negative binomial generalized linear mixed models) based estimates of gene counts from models using different normalization strategies. ensemblid: Ensembl gene identifiers; normalization_model: Indicates normalization model: lib_size_normalized, gene counts are modeled with study conditions as fixed effects and participant id as random effects and with the addition of library size as a fixed effect. tissue_offset_lib_size_normalized, same as lib_size_normalized but with the addition of tissue weight used in library prep as an offset. The non-normalized model is not included in the data set; interaction_model: Indicates if the coefficient is estimated in a model containing the interaction between volume condition and time. If FALSE, the model only contains time as a fixed effect (in addition to any normalization, see above), coefficients should in this case be interpreted as averages over volume conditions; coefficient: Names of coefficients (fixed effects, time and volume conditions). timew2pre and timew12 indicate differences from timew0 (intercept) in rested state models. timew2post indicates differences from timew2pre (intercept) in acute exercise models. setsmultiple indicates interaction effects, the difference between setssingle (reference level) and setsmultiple; estimate: Estimates on the natural log scale; se: Standard errors (SE) on the natural log scale; zvalue: Z-values; pvalue: Un-adjusted P-values; pvalue_adjust: Adjusted P-values (FDR) per model/normalization method and coefficient.