refGroup          package:diffGeneAnalysis          R Documentation

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_v_a_r_i_a_b_i_l_i_t_y (_S_t_a_n_d_a_r_d _E_r_r_o_r)

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

     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.

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

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

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

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.

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

     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.

_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.

_N_o_t_e:

     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.

_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:

     #refGroup(bAdjusted,7,3,4,0.05)

