refGroup: Reference Group computes a robust estimate of inter-assay...
In diffGeneAnalysis: Performs differential gene expression Analysis

Description Usage Arguments Details Value Note Author(s) References Examples

refGroup takes a normalized, bias adjusted dataset and computes a robust estimate of inter-assay variability (Standard Error).This value is used here to perform T-tests. It can also be used in sample size calculations.The associative analysis method is then applied to the computed refernce group.

1	refGroup(biasAdjusted, numSlides, ctrl, exp, pval)

`biasAdjusted`	biasAdjusted is a matrix of bias adjusted normalized microarray data.The first row consists of headers and the first column must consist of Gene Bank Id's.
`numSlides`	numSlides represents the total number of chips in a microarray dataset including control and experiment.
`ctrl`	ctrl represents the total number of ctrl chips in the microarray.
`exp`	exp represents the total number of experiment chips in the microarray.
`pval`	pval is the strigency value for computing the reference group. 0.05 is the normally suggested value.

AssociativeAnalysis performs the Associative-T method of differential gene analysis.The user is asked to enter values for E and R.E stand for the increase in fold over background and R stands for the ratio of experimental chips average over control chips average. The higher these values the higher will be the stringency. Example dataset used here was run with an E values of 1 and R value of 1.5.

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.

refGroup takes 4-5 seconds to execute under optimal conditions of size of datasets and speed of the machine.Tested on Pentium IV 1.6Ghz, 256 MB RAM with 22464 genes and 10 chips it took 25 seconds to execute.

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