assocAnalysis        package:diffGeneAnalysis        R Documentation

_A_s_s_o_c_i_a_t_i_v_e _A_n_a_l_y_s_i_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

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.

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

     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.

_A_u_t_h_o_r(_s):

     Choudary L Jagarlamudi

_R_e_f_e_r_e_n_c_e_s:

     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

_E_x_a_m_p_l_e_s:

     #see refGroup for more details

