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**proteomics**: Statistical Analysis of High Throughput Proteomics Data**testing**: Data Analysis - Testing features with Tukey Honest...

# Data Analysis – Testing features with Tukey Honest Significant Differences

### Description

Data Analysis – Testing features with Tukey Honest Significant Differences

### Usage

1 | ```
testing(dp, frm, conf.level)
``` |

### Arguments

`dp` |
iTRAQ data in long format |

`frm` |
formal for the test |

`conf.level` |
confidence level |

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- accum: Response calculation
- accum: Response calculation
- addIonSatistics: Summary statistics - Ion intensities per spectra
- addIonSatistics: Summary statistics - Ion intensities per spectra
- addLoadings: Adjust for confounding - add an appropiate target
- addLoadings: Adjust for confounding - add an appropiate target
- addRetentionAtApex: Summary statistics - Calculates retention time statistics at...
- addRetentionAtApex: Summary statistics - Calculates retention time statistics at...
- addRetentionIndexTimeStatistics: Summary statistics - Calculates index retention time...
- addRetentionIndexTimeStatistics: Summary statistics - Calculates index retention time...
- adjustBy: Adjust for confounding - Generic function for centring data
- adjustBy: Adjust for confounding - Generic function for centring data
- adjusting: Adjust for confounding - State of the art adjustments for...
- adjusting: Adjust for confounding - State of the art adjustments for...
- adjustOne: Adjust for confounding - In one single experiment only
- adjustOne: Adjust for confounding - In one single experiment only
- avrgLoading: Adjust for confounding - calculates the average loading
- avrgLoading: Adjust for confounding - calculates the average loading
- channelResponses: Response calculation
- channelResponses: Response calculation
- copyLoadings: Adjust for confounding - copy loadings from one experiment to...
- copyLoadings: Adjust for confounding - copy loadings from one experiment to...
- factoring: Sample design - Generating multiple factor designs from...
- factoring: Sample design - Generating multiple factor designs from...
- meetSelection: Data parsing - from Proteom Discover v1.4
- meetSelection: Data parsing - from Proteom Discover v1.4
- mergeFrames: Merging multiple experiments
- mergeFrames: Merging multiple experiments
- norm2Reference: Response calculation
- norm2Reference: Response calculation
- pAction: Plotting p-value distributions
- pAction: Plotting p-value distributions
- plotMePeptide: Plot interaction plots of peptides
- plotMePeptide: Plot interaction plots of peptides
- plotMeProtein: Plot interaction plots of proteins
- plotMeProtein: Plot interaction plots of proteins
- pRetention: Plot Retention Time Statistics
- pRetention: Plot Retention Time Statistics
- pVioline: Plot Retention Time Statistics in violine form
- pVioline: Plot Retention Time Statistics in violine form
- pVolcano: Volcano plot
- pVolcano: Volcano plot
- responseStatisics: Summary statistics - Generic to calculate summary statistics
- responseStatisics: Summary statistics - Generic to calculate summary statistics
- selectByConfidence: Result filtering - Test for biological effect
- selectByConfidence: Result filtering - Test for biological effect
- selectByEffect: Result filtering - Test for biological effect
- selectByEffect: Result filtering - Test for biological effect
- selectByFDR: Result filtering
- selectByFDR: Result filtering
- testForPeptideEffect: Data Analysis - Testing on peptide level
- testForPeptideEffect: Data Analysis - Testing on peptide level
- testForProteinEffect: Data Analysis - Testing on protein level
- testForProteinEffect: Data Analysis - Testing on protein level
- testing: Data Analysis - Testing features with Tukey Honest...
- testing: Data Analysis - Testing features with Tukey Honest...
- testingOneshot: Data Analysis - Testing one feature without Tukey Honest...
- testingOneshot: Data Analysis - Testing one feature without Tukey Honest...
- testingTukey: Data Analysis - Testing one feature with Tukey Honest...
- testingTukey: Data Analysis - Testing one feature with Tukey Honest...
- toAlpha: Measuring stability - angle of loading vector
- toAlpha: Measuring stability - angle of loading vector
- toProportions: Transformation - From intensity scales to density histrograms
- toProportions: Transformation - From intensity scales to density histrograms