LINCS PCCSE Data Processing and Levels

LINCS espouses the concept of making different data levels available for public use.  Different data levels correspond different steps along our processing workflow.  The LINCS PCCSE levels are defined as follows:

Level 0 - Raw Mass Spectrometry Data (LCMS) - will be available through a chorusproject.org repository in the future

Level 1 - Probe Reads (SKY) - Curated Skyline documents; available on this website, including metadata

Level 2 - Raw Numerical Data (RPT) - Matrix data of extracted signal ratios of endogenous probes vs. internal standards; available on this website, including metadata

Level 3 - Normalized and QC'ed Numerical Data (QCNORM) - Matrix data derived from Level 2 after automated processing and normalization

Level 4 - Differential Quantification (DIFF) - Matrix data of Level 3 with plate-wide median ratio of each analyte subtracted from each sample; available on this website, including metadata 

These data levels are mapped onto our processing pipeline as depicted below:

TIP: To browse and access our data sets, hover over the "LINCS" folder in the upper left corner:






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