Normalized protein expression data

Median-MAD normalized protein expression (PROT) data used for visualization and differential analysis

Usage

PROT_CORTEX_NORM_DATA

PROT_SKMGN_NORM_DATA

PROT_HEART_NORM_DATA

PROT_KIDNEY_NORM_DATA

PROT_LUNG_NORM_DATA

PROT_LIVER_NORM_DATA

PROT_WATSC_NORM_DATA

Format

A data frame with protein IDs in rows (feature_ID) and samples in columns (viallabel)

An object of class data.frame with 5999 rows and 61 columns.

An object of class data.frame with 9184 rows and 64 columns.

An object of class data.frame with 9852 rows and 64 columns.

An object of class data.frame with 10877 rows and 64 columns.

An object of class data.frame with 9791 rows and 63 columns.

An object of class data.frame with 9964 rows and 64 columns.

Source

pass1b-06/analysis/proteomics-untargeted/prot-pr/normalized-data/*med-mad-normalized-logratio.txt

Details

Log2 TMT ratios to the common reference were used as quantitative values for all proteomics features (proteins, phosphosites, acetylsite, and ubiquitylsites). Proteomics features not fully quantified in at least two plexes within a tissue and non-rat contaminants were removed. Log2 TMT ratios were sample-normalized by median-centering and mean absolute deviation scaling. Plex batch effects were removed using linear models implemented by the limma::removeBatchEffect().