test.pairwise: Example of output from groupComparisonTMT function

In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Example of output from groupComparisonTMT function

Description

It is the output of groupComparisonTMT function, which is made from quant.pd.msstats. It is a list that consists of the following elements: (1) ComparisonResult: statistical testing results; (2) FittedModel: the fitted linear models ComparisonResult should include the columns as below.

Usage

test.pairwise

Format

A data frame with 60 rows and 7 variables.

Details

• Protein : Protein ID

• Label: Label of the pairwise comparision or contrast

• log2FC: Log2 fold change

• SE: Standard error of the comparsion of contrast results

• DF: Degree of freedom

• pvalue: Value of p statistic of the test

• adj.pvalue: adjusted p value

• issue: used for indicating the reason why a comparison is not testable. NA means the comparison is testable. 'oneConditionMissing' means the protein has no measurements in one conndition of the comparison. Furtherone, when 'issue = oneConditionMissing', 'log2FC = Inf' means the negative condition (with coefficient -1 in the Label column) is missing and 'log2FC = -Inf' means the positive condition (with coefficient 1 in the Label column) is missing. completeMissing' means the protein has no measurements in all the connditions of the comparison. unfittableModel' means there is no enough measurements to fit the linear model. In other words, each condition has only one measurement.

Examples

head(test.pairwise$ComparisonResult)

Vitek-Lab/MSstatsTMT documentation built on Oct. 19, 2024, 1:14 a.m.