Description Usage Arguments Details Value Author(s) References Examples

assocAnalysis performs the Associative-T method of differential gene analysis.

1 2 | ```
assocAnalysis(bAdjusted, numSlides, ctrl, exp, sdrefgrp,
pctrl, pexpm,ctrlavjs, expmavjs, ctrlsds, expmsds, rgrplen)
``` |

`bAdjusted` |
bAdjusted is a matrix of bias adjusted normalized microarray data. |

`numSlides` |
numSlides represents the total number of chips in the microarray experiment. |

`ctrl` |
ctrl is the number of control chips in the microarray experiment. |

`exp` |
exp is the number of control chips in the microarray experiment. |

`sdrefgrp` |
standard deviation of the computed refernce group. |

`pctrl` |
p values of the control chips on performin ttests. |

`pexpm` |
p values of the experiment chips on performin ttests. |

`ctrlavjs` |
averages of genes across all control chips. |

`expmavjs` |
averages of genes across all experiment chips. |

`ctrlsds` |
standard deviations of genes across all control chips. |

`expmsds` |
standard deviations of genes across all experiment chips. |

`rgrplen` |
total number of genes of the computed refernce group. |

AssociativeAnalysis performs the Associative-T method of differential gene analysis.The results are displayed in a 10 column matrix as follows

Column Representation.

1 Gene Bank Id

2 Average Signal of the Control Chips/Channels.

3 SD of Control Chips/Channels.

4 Probability that a given gene in the Control Chips/Channels belongs or does not belong to background.

5 Average Signal of the Experimental Chips/Channels.

6 SD of Experimental Chips/Channels.

7 Probability that a given gene in the Experimental Chips/Channels belongs or does not belong to background.

8 P-value from a Student T-test.

9 P-value from an Associative T-test.

10 Ratio of mean expression values (Control/Experimental).

11 Group Number.

Group Numbers are defined as follows:.

A1 Expressed above background in both sample types, but over-expressed on the Experimental Chips/Channels.

A2 Expressed above background in both sample types, but over-expressed on the Control Chips/Channels.

A3 Expressed above background only on the Experimental Chips/Channel.

A4 Expressed above background only in the Control Chips/Channel.

0 None of the above.

A matrix of 11 columns as described in the details and n rows where n stands for the number of genes in the microarray dataset.

Choudary L Jagarlamudi

Dozmorov I,Centola,M. An associative analysis of gene expression array data.Bioinformatics.2003 Jan22;19(2):204-11

Knowlton N,Dozmorov I, Centola M. Microarray data Analysis Tool box(MDAT): for normalization,adjustment and analysis of gene expression data.Bioonformatics. 2004 Dec 12;20(18):3687-90

1 | ```
#see refGroup for more details
``` |

diffGeneAnalysis documentation built on Nov. 1, 2018, 5 a.m.

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