diffGeneAnalysis (version 1.54.0)

assocAnalysis: Associative Analysis

Description

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

Usage

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

Arguments

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.

Value

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.

Details

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.

References

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

Examples

#see refGroup for more details