lgatto / 2016-10-rbioc-prot-stellenbosch

Material for R/Bioconductor Proteomics Workshop at Stellenbosch University, October 2016

Material for R/Bioconductor Proteomics Workshop at Stellenbosch University, October 2016

Short URL to this page: http://bit.ly/2016-rbiocprot-sun

Material

• Introduction to R/RStudio
• R/Bioconductor for proteomics
• Data visualisation
• mzR and MSnbase packages for raw data
• Identification data in mzR, mzID, MSnID
• The MSnbase package: MSnSets for quantitative proteomics
• Experimental designs: biological and technical variability, blocking and randomisation
• Handling missing values in proteomics data
• Differential expression of proteomics data (t-test for continuous data, count data, limma)
• Multiple testing
• Wrap-up

Schedule

time	Tue.25.Oct	Wed.26.Oct	Thu.27.Oct
9:00 - 10:00	R/RStudio intro (LG)	Identification 1: DB Search and other methods (DT)	Advanced quant: Technology selection, Power, Biofluids (DT)
10:00 - 11:00	R (LG)	Practical (DT)	Bridget Calder, UCT, demos Skyline
11:00 - 11:30	Coffee	Coffee	Coffee
11:30 - 12:30	R/Bioconductor for proteomics (LG)	Identification 2: protein inference and controlling FDR (DT)	Missing values (lecture + demo/practical) (LG)
12:30 - 13:30	Lunch	Lunch	Lunch
13:30 - 14:30	MS data: pwiz and quameter (DT)	R/Bioconductor: mzR, mzID, MSnID (LG)	Differential expression (t-test for continuous data, count data, limma) (LG)
14:30 - 15:30	Data visualisation (LG)	Intro: quantitative proteomics (DT)	Multiple testing (LG)
15:30 - 16:00	Coffee	Coffee	Coffee
16:00 - 17:00	Practical with R: the mzR and MSnbase packages for raw data (LG)	The MSnbase package: MSnSets for quantitative proteomics (LG)	Wrap-up

LG: Laurent Gatto - DT: David Tabb

Related material and references

• Teaching material

• Gatto L. and Christoforou A. Using R and Bioconductor for proteomics data analysis, Biochim Biophys Acta - Proteins and Proteomics, 2013. PMID:23692960 (preprint)

• Gatto L, Breckels LM, Naake T, Gibb S. Visualisation of proteomics data using R and Bioconductor. Proteomics. 2015 Feb 18. doi: 10.1002/pmic.201400392. PMID:25690415.

• Gatto L. and Lilley K.S. MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualisation, processing and quantitation, Bioinformatics, 28(2), 288-289, 2012 PMID:22113085

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