ProteoSign README file

Dear User, please find below a short description for each ProteoSign output file.

Log file (log.txt):
	This file is generated by the core statistical analysis R script and can be used by the software authors for troubleshooting in problematic cases.

condition-i vs condition-j file (<...>condition-i_vs_condition-j<...>.txt):
	This table constitutes part of the core output of the statistical analysis software (LIMMA). For each protein, it shows: 
		Column A: the average log2 intensity across conditions and replicates. 
		Column Coef: the estimate of the log2-fold-change. 
		Column t: the moderated t-statistic. 
		Column p.value: the raw p-value corresponding to the t-statistic. 
		Column p.value.adj: the adjusted p-value. 
		Column F: the moderated F-statistic. 
		Column F.p.value: the p-value corresponding to the F-statistic.

Blocking variable file (<...>limma-blocking-variable<...>.txt):
	Indicates the technical replicates in the design matrix file (described below). This file is for diagnostic purposes only.

Design matrix file (<...>limma-design-matrix<...>.txt):
	Table showing the contents of the design matrix. This file is for diagnostic purposes only.

Contrasts matrix file (<...>limma-contrast-matrix<...>.txt):
	Specifies which comparisons between the linear model coefficients are of interest. This file is for diagnostic purposes only.

Quantified proteins list file (<...>quant-venn3-data-2reps<...>.txt):
	Table listing the proteins quantified in each biological replicate. Can be used to construct a Venn diagram.

LIMMA input file (<...>limma-input_ProteinGroups.txt):
	Table showing the pre-processed data that were subjected to log-transformation and quantile-normalization before being sent for analysis to the core statistics software (LIMMA). This file is for diagnostic purposes only.

LIMMA early input file (<...>proteinGroupsDF.txt):
	Table showing an early version of the data that were sent for analysis to the core statistics software (LIMMA). This file is for diagnostic purposes only.

Identified proteins list file (<...>id_venn3-data<...>.txt):
	Table listing the proteins identified in each biological replicate. Can be used to construct a Venn diagram.

Results file (<...>results<...>.txt):
	The statistical analysis main output file. For each protein, information about the expression ratio between conditions and its significance level are given.

Top results file (<...>diffexp<...>.txt):
	A trimmed version of the aforementioned results file comprising only the statistically significant results (differentially expressed proteins).

Pre-normalization intensities PDF file (contained in <...>limma-graphs<...>.pdf):
	Box plots of log2 protein intensities before quantile normalization for each replicate and condition.

Post-normalization intensities PDF file (contained in <...>limma-graphs<...>.pdf):
	Box plots of log2 protein intensities after quantile normalization for each replicate and condition.

Log2-fold change histogram PDF file (contained in <...>limma-graphs<...>.pdf):
	Histogram of Log2 protein intensity ratio.

MA plot PDF file (<...><conditioni>.<conditionj>-MA<...>.pdf):
	Scatter plot of average log2 protein intensity ratio in condition i against average log2 intensity in condition j (also known as MA plot).

Intensities scatter plot matrix PDF file (<...><conditioni>.<conditionj>-reproducibility<...>.pdf):
	Scatter plots and linear regression lines, histograms, and Pearson's R values for each combination of replicate log2 protein intensity ratio.

Value-ordered fold change PDF file (<...><conditioni>.<conditionj>-value-ordered-log-ratio<...>.pdf):
	Plot of Protein number (ID) against log2 intensity ratio.

Volcano plot PDF file (<...><conditioni>.<conditionj>-volcano<...>.pdf):
	Plot of average log2 protein intensity ratio against -log10 p-value (also known as volcano plot) .

Plot Generator R Script and object file (Plot_Generator.R and Plot_Generator.RData):
	The file Plot_Generator.R can be edited and run by an experienced user in R in order to produce the results plots manually and change their appeareance as desired. An R objects file with the same name is contained in the ZIP archive and stores all the data needed by the script.

Parameters file (<...>parameters_from_session<...>.txt)
	This text file contains the entire set of user-defined parameters during the ProteoSign session/run. The user should not modify this file but rather upload it in another session in order to reload the values of the comprised parameters.

For more information please refer to our help page.