Processed immunoassay data used for differential analysis

Normalized, imputed, and filtered multiplexed immunoassay data used for differential analysis

Usage

IMMUNO_NORM_DATA_NESTED

Format

A nested list of data frames

Source

mawg-data/pass1b-06/immunoassay/data/release/pass1b-06*_mfi-log2-filt-imputed-na-outliers.txt

Details

IMMUNO sample-level data is in a different format than sample-level data for other assays/omes. Extract data from a panel and tissue using IMMUNO_NORM_DATA_NESTED[[dataset]][[tissue]], where dataset is one of "ADIPONECTIN", "SERPIN-E", "rat-mag27plex", "rat-metabolic", "rat-myokine", "rat-pituitary", and tissue is a tissue abbreviation (see TISSUE_ABBREV). Samples (vial labels) are in rows, and analytes are in columns. Column names, barring the first "viallabel" column, correspond to feature_IDs.

Raw mean fluorescent intensities (MFIs) were log2-transformed, and measurements corresponding to wells with less than 20 beads were removed. For remaining measurements in each panel and tissue, samples with more than 50\ features with at least two missing values for a single experimental group (e.g., males trained for 2 weeks) were removed (this affected four colon analytes and one spleen analyte, all in the rat-mag27plex panel). Remaining missing values were imputed with k-nearest neighbors (k=5 features). Within each panel, tissue, and analyte, we calculated the mean and standard deviation and removed outlying measurements more than 4 standard deviations away from the mean. This is the version of the data provided by this object and used for differential analysis.

SERPIN-E and ADIPONECTIN were both originally in a panel called rat-adipokine. They were split into their own "panels" because this panel was run with two dilutions, and one was optimal for SERPIN-E while the other was optimal for ADIPONECTIN. Hence, in some places dataset refers to "rat-adipokine" while in other places, like here, dataset refers to "SERPIN-E" or "ADIPONECTIN", among others.