3.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 into R 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 containing all the original columns, 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.

_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 gene
     name and annoation information in a separate file. The function
     'readGAL' reads information from a GenePix Allocation List (gal)
     file. It produces a data frame with known column names. If the
     gene names consist of a short name followed by annotation
     information, 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.

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

     'cbind' allows different 'RGList' or 'MAList' objects to be
     combined assuming the layout of the arrays to be the same. 'merge'
     can combine data even when the order of the genes on the arrays
     has changed. 'merge' uses utility function 'makeUnique'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

