03.ReadingData             package:limma             R Documentation

_R_e_a_d_i_n_g _M_i_c_r_o_a_r_r_a_y _D_a_t_a _f_r_o_m _F_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This help page gives an overview of LIMMA functions used to read
     data from files.

_R_e_a_d_i_n_g _T_a_r_g_e_t _I_n_f_o_r_m_a_t_i_o_n:

     The function 'readTargets' is designed to help with organizing
     information about which RNA sample is hybridized to each channel
     on each array and which files store information for each array.

_R_e_a_d_i_n_g _I_n_t_e_n_s_i_t_y _D_a_t_a:

     The first step in a microarray data analysis is to read into R the
     intensity data for each array provided by an image analysis
     program. This is done using the function 'read.maimages'.

     'read.maimages' optionally constructs quality weights for each
     spot using quality functions listed in QualityWeights.

     'read.maimages' produces an 'RGList' object and stores only the
     information required from each image analysis output file.
     'read.maimages' uses utility functions 'removeExt', 'read.imagene'
     and 'read.columns'. There are also a series of utility functions
     which read the header information from image output files
     including 'readGPRHeader', 'readImaGeneHeader' and
     'readGenericHeader'.

     The function as.MAList can be used to convert a 'marrayNorm'
     object to an 'MAList' object if the data was read and normalized
     using the marray and marrayNorm packages.

_R_e_a_d_i_n_g _t_h_e _G_e_n_e _L_i_s_t:

     Most image analysis software programs provide gene IDs as part of
     the intensity output files, for example GenePix, Imagene and the
     Stanford Microarray Database do this. In other cases the probe ID
     and annotation information may be in a separate file. The most
     common format for the probe annotation file is the GenePix Array
     List (GAL) file format. The function 'readGAL' reads information
     from a GAL file and produces a data frame with standard column
     names.

     The function 'getLayout' extracts from the GAL-file data frame the
     print layout information for a spotted array. The functions
     'gridr', 'gridc', 'spotr' and 'spotc' use the extracted layout to
     compute grid positions and spot positions within each grid for
     each spot. The function 'printorder' calculates the printorder,
     plate number and plate row and column position for each spot given
     information about the printing process. The utility function
     'getSpacing' converts character strings specifying spacings of
     duplicate spots to numeric values.

     The Australian Genome Research Facility in Australia often
     produces GAL files with composite probe IDs or names consisting of
     multiple strings separated by a delimiter. These can be separated
     into name and annotation information using 'strsplit2'.

     If each probe is printed more than once of the arrays in a regular
     pattern, then 'uniquegenelist' will remove duplicate names from
     the gal-file or gene list.

_I_d_e_n_t_i_f_y_i_n_g _C_o_n_t_r_o_l _S_p_o_t_s:

     The functions 'readSpotTypes' and 'controlStatus' assist with
     separating control spots from ordinary genes in the analysis and
     data exploration.

_M_a_n_i_p_u_l_a_t_i_n_g _D_a_t_a _O_b_j_e_c_t_s:

     'cbind', 'rbind', 'merge' allow different 'RGList' or 'MAList'
     objects to be combined. 'cbind' combines data from different
     arrays assuming the layout of the arrays to be the same. 'merge'
     can combine data even when the order of the probes on the arrays
     has changed. 'merge' uses utility function 'makeUnique'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

