Omics Data QA/QC tool

Authors:

Nurgul Kaplan¹,Yan Chen¹,Jennifer Gin¹,Christopher Petzold¹

¹Lawrence Berkeley National Laboratory

Omics Data QA/QC tool step by step tutorial:

Step 1:

Run the script to generate:

Full, summary reports
Bar, Line Visuals (per type)
Data Quality Visuals
- Scatter Plot
- Violin plot

Step 2:

Optinal: Run the script to analyze different protocols:

By default, the script will analyze the first protocol in the dataset. If there are multiple protocols, please identify the protocol in dropdown menu.

Targeted Proteomics
Metabolomics
HPLC

Step 3:

Optinal: Run the script to exclude certain assays:

By default, the script will analyze ALL of the assays in the dataset. Specific assays can be excluded from the analysis via selection if desired.

Step 4:

Optional: Run the script to modify cutoff peak area:

Users have an option to input an intensity threshold to exclude data with values less than the cutoff line. There is a live feedback of the action by showing the number and the percentage of remaining data points.

Note: If there are no replicates in the study, the Data Quality script will not generate Scatter or Violin plots.

If there are replicates in the dataset, scatter and violin plots will be generated with the complete dataset.

For more information, please email ese-robotics@lbl.gov

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