Description Usage Arguments Details Value Note Examples

Calculate aFold for each gene and general sd

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`nncounts` |
matrix for read count. |

`cond` |
factor for conditions. If provide only one condition, fold-change estimation will be suppressed. |

`preval` |
pre-defined scale control for variance normalization, default is 0.05, a large value generally increases the fold-changes (decreases penalty of variances) under low expression. |

`qforkappa` |
quantile for estimating kappa(>=qforkappa), default is 0 (without trimming of data). Please set up a value in [0,1) if you want to trim the low expressed data. |

`pair` |
switch for paired samples, default is false |

`priorgenesd` |
prior value for general SD of fold change, if provided, the estimation of general SD will be replaced by this value. |

shifted and calculate a set of parameters from normalized counts table before `callDEs`

A list with log2 foldchange, general SD for calculating pvalue, variance stabilized counts and expression level adjusted counts (used for PCA analysis)

This function should run after `normalFactors`

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