The SafeQuant Package includes methods for analysis of quantitative (LFQ,TMT,HRM) Proteomics data.
A) Install CRAN library dependencies (open R)
R> install.packages(c("seqinr","gplots","corrplot","optparse","data.table","epiR"))
B) Install BioConductor library dependencies (open R)
R> source("http://bioconductor.org/biocLite.R")
R> biocLite(c("limma","affy"))
Option 1, install "master branch" using "devtools"
Make sure you have a working development environment.
Windows: Install Rtools.
Mac: Install Xcode from the Mac App Store.
Linux: Install a compiler and various development libraries (details vary across different flavors of Linux).
R> install.packages("devtools")
R> library(devtools)
R> install_github("eahrne/SafeQuant")
Option 2, install latest CRAN version
R> install.packages("SafeQuant")
A) locate file safeQuant.R (C:\Users\ahrnee-adm\Downloads\SafeQuant\exec\safeQuant.R ) This is the SafeQuant main script. Copy it to an appropriate directory, e.g. c:\Program Files\SafeQuant\
B) open terminal To display help options
> Rscript "c:\Program Files\SafeQuant\safeQuant.R" -h
To run (with minimal arguments)
> Rscript "c:\Program Files\SafeQuant\safeQuant.R" -i "c:\Program Files\SafeQuant\testData\peptide_measurement.csv" -o "c:\Program Files\SafeQuant\out"
I) If using Progenesis QI we advice running SafeQuant on "Peptide Measurement" Exports. - File -> Export Peptide Measurements. This option is available once you have reached the "Resolve Conflicts" Step in Progenesis QI - When choosing properties to be included in the exported file check the "Grouped accessions (for this sequence)" check box.
II) When working with Progenesis "Feature Exports" it is advisable to discard all features (rows) not annotated with a peptide, to speed up SafeQuant analysis. This can be done using the "filterLargeProgenesisPeptideFile.pl" perl script. (C:\Users\ahrnee-adm\Downloads\SafeQuant\exec\filterLargeProgenesisPeptideFile.pl)
A) install perl (or activePerl for windows http://www.activestate.com/activeperl)
B) open terminal
> perl "C:\Program Files\SafeQuant\filterLargeProgenesisPeptideFile.pl" "C:\Program Files\SafeQuant\testData\features.csv"
This will create a new versions of the feature file called with the extension "_FILTERED" features.csv -> features_FILTERED.csv
Smyth, G. K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol, 3 SP -, Article3. http://www.ncbi.nlm.nih.gov/pubmed/16646809
https://raw.githubusercontent.com/eahrne/SafeQuant/master/inst/manuals/SafeQuant_UseCases.txt
https://github.com/eahrne/SafeQuant/blob/master/inst/manuals/tsv_spreadsheet_help.pdf
https://github.com/eahrne/SafeQuant/blob/master/inst/manuals/SafeQuant-man.pdf
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.