Informatics and Statistics for Metabolomics 2018
Informatics and Statistics for Metabolomics.
The course schedule can be found here.
Pre-readings, pre-work, and laptop setup instructions can be found here.
We are using Google Classroom for discussion. Join the Class at https://classroom.google.com, select the “+” symbol in the upper right corner, click on “Join Class” and enter the class code provided to you.
The full course notes are available as a single PDF.
Module 1: Introduction to Metabolomics
Module 2: Metabolite Identification and Annotation
NMR and Bayesil.
GC-MS and GCMS.
LC-MS and XCMS in R. If R doesn’t work, try XCMS online.
Data Set and Results Files:
Download this file
Raw datasets (raw.zip files)
Converted datasets (mzxml.zip files)
XCMS using R (results files)
XCMS online (results files)
- BMRB Peaks Server
- Golm Database
- Adduct Table
- 7GR Software
Module 3: Databases for Chemical, Spectral, and Biological Data
Module 4: Backgrounder in Statistics
Module 5: MetaboAnalyst
Critical: before uploading your data, perform a sanity check:
- It is a data table separated by comma (.csv) or tab (.txt);
- Three types of labels: feature names, sample names and group labels (must directly follow sample names);
- All measurements should be numerical values (empty for missing values);
For details and screenshot instructions, click here
- You may have downloaded the NMR results .zip folder yesterday. You will need the .csv file from the .zip folder. NMR results.zip (Bayesil output - need to remove annotations lines starting with #, keep one type of ID - name/HMDB ID)
- Cleaned GCMS results (Auto-GCMS output that has been cleaned for you)
- Normalized LCMS csv
Module 6: Future of Metabolomics
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