Example of output from groupComparisonTMT function

It is the output of groupComparisonTMT function, which is the result of group comparions with the output of proteinSummarization function. It should include the columns as below. The variables are as follows:

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)

#>   Protein       Label       log2FC         SE       DF    pvalue adj.pvalue
#> 1  P04406   0.125-0.5 -0.031373953 0.02184769 111.8928 0.1537834  0.4077350
#> 2  P04406 0.125-0.667 -0.010442843 0.02184769 111.8928 0.6335941  0.9051345
#> 3  P04406     0.125-1 -0.005921016 0.02184769 111.8928 0.7868800  0.9519310
#> 4  P04406   0.5-0.667  0.020931110 0.02184769 111.8928 0.3401046  0.5731751
#> 5  P04406       0.5-1  0.025452937 0.02184769 111.8928 0.2464896  0.6162240
#> 6  P04406     0.667-1  0.004521827 0.02184769 111.8928 0.8364091  0.9321517
#>   issue
#> 1    NA
#> 2    NA
#> 3    NA
#> 4    NA
#> 5    NA
#> 6    NA