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Normalized protein phosphorylation data

Source: R/data.R
PHOSPHO_NORM_DATA.Rd

Median-MAD normalized protein phosphorylation (PHOSPHO) data used for visualization and differential analysis

Usage

PHOSPHO_CORTEX_NORM_DATA

PHOSPHO_SKMGN_NORM_DATA

PHOSPHO_HEART_NORM_DATA

PHOSPHO_KIDNEY_NORM_DATA

PHOSPHO_LUNG_NORM_DATA

PHOSPHO_LIVER_NORM_DATA

PHOSPHO_WATSC_NORM_DATA

Format

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

An object of class data.frame with 29651 rows and 61 columns.

An object of class data.frame with 40208 rows and 64 columns.

An object of class data.frame with 30144 rows and 64 columns.

An object of class data.frame with 47661 rows and 64 columns.

An object of class data.frame with 43567 rows and 63 columns.

An object of class data.frame with 30304 rows and 64 columns.

Source

pass1b-06/analysis/proteomics-untargeted/prot-ph/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().