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. If you
     wish to read all the image analysis output files into R as
     individual data frames preserving all the original columns found
     in the files, you may use 'read.series'. An 'RGList' object can be
     extracted from the data frames at a later stage using the
     functions 'rg.spot', 'rg.genepix' or 'rg.quantarray'.

     Another function, 'rg.series.spot' is very similar to
     'read.maimages' with 'source="spot"'. This function will be
     removed in future versions of LIMMA.

     'read.maimages' uses utility functions 'removeExt', 'read.matrix',
     'read.imagene' and 'readImaGeneHeader'.

     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:

     Many image analysis program provide gene IDs as columns in the
     image analysis output files, for example ArrayVision, Imagene and
     the Stanford Microarray Database. In other cases you may have the
     probe ID and annotation information in a separate file. The
     function 'readGAL' reads information from a GenePix Array List
     (GAL) file. It produces a data frame with known column names. If
     the probe IDs or names consist of multiple strings separated by a
     delimiter, then 'splitName' may be used to separate the name and
     annotation information into separate vectors.

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

     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.

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

_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

