mergeScans               package:limma               R Documentation

_M_e_r_g_e _t_w_o _s_c_a_n_s _o_f _t_w_o-_c_o_l_o_r _a_r_r_a_y_s

_D_e_s_c_r_i_p_t_i_o_n:

     Merge two sets of intensities of two-color arrays that are scanned
     twice at two different scanner settings, one at a lower gain
     setting with no saturated spot intensities and the other at a
     higher gain setting with a higher signal-to-noise ratio and some
     saturated spot intensities.

_U_s_a_g_e:

     mergeScansRG(RGlow, RGhigh, AboveNoiseLowG=NULL, AboveNoiseLowR=NULL, outlierp=0.01)

_A_r_g_u_m_e_n_t_s:

   RGlow: object of class 'RGList' containing red and green intensities
          constituting two-color microarray data scanned at a lower
          gain setting.

  RGhigh: object of class 'RGList' containing red and green intensities
          constituting two-color microarray data scanned at a higher
          gain setting.

AboveNoiseLowG: matrix of 1 or 0 for low scan intensities of green
          color, 1 for spots above noise level or 0 otherwise. One
          column per array.

AboveNoiseLowR: matrix of 1 or 0 for low scan intensities of red color,
          1 for spots above noise level or 0 otherwise. One column per
          array. 

outlierp: p-value for outliers. 0 for no outlier detection or any value
          between 0 and 1. Default p-value is 0.01.

_D_e_t_a_i_l_s:

     This function merges two separate scans of each fluorescent label
     on a two-color array scanned at two different scanner settings by
     using a nonlinear regression model consisting of two linear
     regression lines and a quadratic function connecting the two,
     which looks like a hockey stick. The changing point, i.e. the
     saturation point, in high scan is also estimated as part of model.
     Signals produced for certain spots can sometimes be very low
     (below noise) or too high (saturated) to be accurately read by the
     scanner. The proportions of spots that are below noise or above
     saturation are affected by the settings of the laser scanner used
     to read the arrays, with low scans minimizing saturation effects
     and high scans maximizing signal-to-noise ratios. Saturated spots
     can cause bias in intensity ratios that cannot be corrected for
     using conventional normalization methods.

     Each fluorescent label on a two-color array can be scanned twice:
     for example, a high scan targeted at reaching saturation level for
     the brightest 1 percent of the spots on the array, and a low scan
     targeted at the lowest level of intensity which still allowed
     accurate grid placement on the arrays. By merging data from two
     separate laser scans of each fluorescent label on an array, we can
     avoid the potential bias in signal intensities due to below noise
     or above saturation and, thus provide better estimates of true
     differential expression as well as increase usable spots.

     The merging process is designed to retain signal intensities from
     the high scan except when scanner saturation causes the high scan
     signal to be under-measured. The saturated spots are predicted
     from the corresponding low scans by the fitted regression model.
     It also checks any inconsistency between low and high scans.

_V_a_l_u_e:

     An object of class 'RGList-class' with the following components:

       G: numeric matrix containing the merged green (cy3) foreground
          intensities. Rows correspond to spots and columns to arrays.

       R: numeric matrix containing the merged red (cy5) foreground
          intensities. Rows correspond to spots and columns to arrays.

      Gb: numeric matrix containing the green (cy3) background
          intensities from high scan.

      Rb: numeric matrix containing the red (cy5) background
          intensities from high scan.

   other: list numeric matrices 'Gsaturated', 'Rsatured', 'Goutlier'
          and 'Routlier'. The first two contain saturation flags
          (1=saturated, 0=otherwise) for the green (cy3) and red (Cy5)
          channels of the high scan. The second two contain outlier
          flags (1=outlier, 0=otherwise) for the green (cy3) and red
          (Cy5) channels.

_A_u_t_h_o_r(_s):

     Dongseok Choi choid@ohsu.edu.

_R_e_f_e_r_e_n_c_e_s:

     Choi D, O'Malley JP, Lasarev MR, Lapidus J, Lu X, Pattee P, 
     Nagalla SR (2006). Extending the Dynamic Range of Signal
     Intensities in DNA Microarrays. _Online Journal of
     Bioinformatics_, *7*, 46-56.

_E_x_a_m_p_l_e_s:

     ## Not run: 
     #RG1: An RGList from low scan
     #RG2: An RGList from high scan
     RGmerged <- mergeScansRG(RG1,RG2,AboveNoiseLowG=ANc3,AboveNoiseLowR=ANc5)

     #merge two scans when all spots are above noise in low scan and no outlier detection.
     RGmerged <- mergeScansRG(RG1,RG2,outlierp=0)
     ## End(Not run)