spatial                package:MANOR                R Documentation

_E_x_a_m_p_l_e_s _o_f  _a_r_r_a_y-_C_G_H _d_a_t_a _w_i_t_h _s_p_a_t_i_a_l _a_r_t_i_f_a_c_t_s

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

     This data set provides an example of array-CGH data with spatial
     artifacts, consisting of including 'arrayCGH' objects before and
     after normalization

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

     data(spatial)

_F_o_r_m_a_t:


   _e_d_g_e, _g_r_a_d_i_e_n_t 'arrayCGH' objects before normalization:

            'arrayValues'  spot-level information
            'arrayDesign'  block design of the array
            'cloneValues'  additionnal clone-level data (chromosome, position)


   _e_d_g_e._n_o_r_m, _g_r_a_d_i_e_n_t._n_o_r_m 'arrayCGH' objects after normalization

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

     'edge' presents local spatial bias in the top-right edge corner,
     and 'gradient' presents global spatial trend. 'edge' and
     'gradient' are 'arrayCGH' objects before normalization. They have
     been created respectively from spot and gpr files using 'import'.
     'edge.norm' and 'gradient.norm' are the corresponding 'arrayCGH'
     objects after normalization using 'norm.arrayCGH'.

     'flag' objects used for data normalization come from 'flags'
     dataset.

_N_o_t_e:

     People interested in tools for array-CGH analysis can visit our
     web-page: <URL: http://bioinfo.curie.fr>.

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

     Pierre Neuvial, manor@curie.fr.

_S_o_u_r_c_e:

     Institut Curie, manor@curie.fr.

_S_e_e _A_l_s_o:

     'flags'

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

     data(spatial)

     ## edge: example of array with local spatial effects

     layout(matrix(1:4, 2, 2), height=c(9,1))
     arrayPlot(edge, "LogRatio", main="Log-ratios before normalization",
     zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE)
     arrayPlot(edge.norm, "LogRatioNorm", main="Log-ratios after spatial
     normalization", zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE) 

     ## gradient: example of array with spatial gradient

     layout(matrix(1:4, 2, 2), height=c(9,1))
     arrayPlot(gradient, "LogRatio", main="Log-ratios before normalization",
     zlim=c(-2,2), bar="h", layout=FALSE)
     arrayPlot(gradient.norm, "LogRatioNorm", main="Log-ratios after spatial
     normalization", zlim=c(-2,2), bar="h", layout=FALSE)   

