Differential analysis of multiplexed immunoassays — IMMUNO

Timewise summary statistics and training FDR from differential analysis (DA) that tests the effect of training on each immunoassay analyte within each sex. One data frame per tissue.

Usage

IMMUNO_PLASMA_DA

IMMUNO_HIPPOC_DA

IMMUNO_CORTEX_DA

IMMUNO_ADRNL_DA

IMMUNO_TESTES_DA

IMMUNO_OVARY_DA

IMMUNO_SKMGN_DA

IMMUNO_BAT_DA

IMMUNO_WATSC_DA

IMMUNO_COLON_DA

IMMUNO_SMLINT_DA

IMMUNO_LIVER_DA

IMMUNO_SKMVL_DA

IMMUNO_HEART_DA

IMMUNO_KIDNEY_DA

IMMUNO_SPLEEN_DA

IMMUNO_LUNG_DA

Format

A data frame with 17 variables:

feature: character, unique feature identifier in the format 'ASSAY_ABBREV;TISSUE_ABBREV;feature_ID' only for training-regulated features at 5% IHW FDR. For redundant differential features, 'feature_ID' is prepended with the specific platform to make unique identifiers. See REPEATED_FEATURES for details.
assay: character, assay abbreviation, one of ASSAY_ABBREV
assay_code: character, assay code used in data release. See MotrpacBicQC::assay_codes.
tissue: character, tissue abbreviation, one of TISSUE_ABBREV
tissue_code: character, tissue code used in data release. See MotrpacBicQC::bic_animal_tissue_code.
feature_ID: character, MoTrPAC feature identifier
dataset: character, name of LUMINEX panel, e.g., 'rat-mag27plex'
sex: character, one of 'male' or 'female'
comparison_group: character, time point of trained animals compared to the sex-matched sedentary control animals, one of '1w', '2w', '4w', '8w'
p_value: double, unadjusted p-value for the difference between 'comparison_group' and the group of sex-matched sedentary control animals
adj_p_value: double, adjusted p-value from 'p_value' column. P-values are BY-adjusted across all datasets within a given assay/ome.
logFC: double, log fold-change where the numerator is 'comparison_group', e.g., '1w', and the denominator is the group of sex-matched sedentary control animals
logFC_se: double, standard error of the log fold-change
covariates: character, comma-separated list of adjustment variables or NA
comparison_average_intensity: double, average intensity among the replicates in 'comparison_group'
reference_average_intensity: double, average intensity among the replicates in the group of sex-matched sedentary control animals
selection_fdr: double, adjusted training p-value used to select training-regulated analytes. P-values are IHW-adjusted across all datasets within a given assay with tissue as a covariate.

An object of class data.frame with 368 rows and 17 columns.

An object of class data.frame with 184 rows and 17 columns.

An object of class data.frame with 424 rows and 17 columns.

An object of class data.frame with 280 rows and 17 columns.

An object of class data.frame with 312 rows and 17 columns.

An object of class data.frame with 216 rows and 17 columns.

An object of class data.frame with 208 rows and 17 columns.

An object of class data.frame with 216 rows and 17 columns.

Details

Reproduce our analysis with MotrpacRatTraining6mo::immuno_timewise_da() and MotrpacRatTraining6mo::immuno_training_da().