Description Usage Arguments Details Value Author(s) References See Also Examples

'GetMultiFC' calculates the Fold Changes for each pair of conditions in a multiple condition study.

1 | ```
GetMultiFC(EBMultiOut, SmallNum = 0.01)
``` |

`EBMultiOut` |
The output of EBMultiTest function. |

`SmallNum` |
A small number will be added for each transcript in each condition to avoid Inf and NA. Default is 0.01. |

Provide the FC (adjusted by the normalization factors) for each pair of comparisons. A small number will be added for each transcript in each condition to avoid Inf and NA. Default is set to be 0.01.

`FCMat` |
The FC of each pair of comparison (adjusted by the normalization factors). |

`Log2FCMat` |
The log 2 FC of each pair of comparison (adjusted by the normalization factors). |

`PostFCMat` |
The posterior FC of each pair of comparison. |

`Log2PostFCMat` |
The log 2 posterior FC of each pair of comparison. |

`CondMean` |
The mean of each transcript within each condition (adjusted by the normalization factors). |

`ConditionOrder` |
The condition assignment for C1Mean, C2Mean, etc. |

Ning Leng

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

EBMultiTest, PostFC

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
data(MultiGeneMat)
MultiGeneMat.small = MultiGeneMat[201:210,]
Conditions = c("C1","C1","C2","C2","C3","C3")
PosParti = GetPatterns(Conditions)
Parti = PosParti[-3,]
MultiSize = MedianNorm(MultiGeneMat.small)
MultiOut = EBMultiTest(MultiGeneMat.small,
NgVector=NULL, Conditions=Conditions,
AllParti=Parti, sizeFactors=MultiSize,
maxround=5)
MultiFC = GetMultiFC(MultiOut)
``` |

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