compareLimmapumaDE           package:puma           R Documentation

_C_o_m_p_a_r_e _p_u_m_a_D_E _w_i_t_h _a _d_e_f_a_u_l_t _L_i_m_m_a _m_o_d_e_l

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

     This function compares the identification of differentially
     expressed (DE) genes using the 'pumaDE' function and the 'limma'
     package.

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

     compareLimmapumaDE(
             eset_mmgmos
     ,       eset_comb = NULL
     ,       eset_other = eset_mmgmos
     ,       limmaRes = calculateLimma(eset_other)
     ,       pumaDERes = pumaDE(eset_comb)
     ,       contrastMatrix = createContrastMatrix(eset_mmgmos)
     ,       numberToCompareForContrasts = 3
     ,       numberToCompareForVenn = 100
     ,       plotContrasts = TRUE
     ,       contrastsFilename = NULL
     ,       plotOther = FALSE
     ,       otherFilename = "other"
     ,       plotBcombContrasts = FALSE
     ,       bcombContrastsFilename = "bcomb_contrasts"
     ,       plotVenn = FALSE
     ,       vennFilename = "venn.pdf"
     ,       showTopMatches = FALSE
     ,       returnResults = FALSE
     )

_A_r_g_u_m_e_n_t_s:

eset_mmgmos: An object of class 'ExpressionSet', that includes both
          expression levels as well as standard errors of the
          expression levels. This will often have been created using
          'mmgmos', but might also have been created by 'mgmos', or any
          other method capable of providing standard errors. 

eset_comb: An object of class 'ExpressionSet', includes both expression
          levels as well as standard errors of the expression levels
          for each unique condition in an experiment (i.e. created from
          combining the information from each replicate). This will
          usually have been created using  'pumaComb'. 

eset_other: An object of class 'ExpressionSet', that includes
          expression levels , and may optionally also include standard
          errors of the expression levels. This is used for comparison
          with 'eset_mmgmos', and might have been created by any
          summarisation method, e.g. 'rma'. 

limmaRes: A list with two elements, usually created using the function
          'calculateLimma'. The first element is a matrix of p-values.
          Each column represent one contrast. Within each column the
          p-values are ordered. The second element is a matrix of row
          numbers, which can be used to map p-values back to probe
          sets. If not supplied this will be automatically created from
          'eset_other'. 

pumaDERes: A list with two elements, usually created using the function
          'pumaDE'. The first element is a matrix of PPLR values. Each
          column represent one contrast. Within each column the PPLR
          values are ordered. The second element is a matrix of row
          numbers, which can be used to map PPLR values back to probe
          sets. If not supplied this will be automatically created from
          'eset_comb'. 

contrastMatrix: A contrast matrix. If not supplied this will be created
          from 'eset_mmgmos' 

numberToCompareForContrasts: An integer specifying the number of most
          differentially expressed probe sets (genes) that will be used
          in comparison charts. 

numberToCompareForVenn: An integer specifying the number of most
          differentially expressed probe sets (genes) that will be used
          for comparison in the Venn  diagram. 

plotContrasts: A boolean specifying whether or not to plot the most
          differentially expressed probe sets (genes) for each contrast
          for the 'eset_mmgmos' 'ExpressionSet'. 

contrastsFilename: A character string specifying a file name stem for
          the PDF files which will be created to hold the contrast
          plots for the 'eset_mmgmos' 'ExpressionSet'. The actually
          filenames will have the name of the contrast appended to this
          stem. 

plotOther: A boolean specifying whether or not to plot the most
          differentially expressed probe sets (genes) for each contrast
          for the 'eset_other' 'ExpressionSet'. 

otherFilename: A character string specifying a file name stem for the
          PDF files which will be created to hold the contrast plots
          for the 'eset_other' 'ExpressionSet'. The actually filenames
          will have the name of the contrast appended to this stem. 

plotBcombContrasts: A boolean specifying whether or not to plot the
          most differentially expressed probe sets (genes) for each
          contrast for the 'eset_comb' 'ExpressionSet'. 

bcombContrastsFilename: A character string specifying a file name stem
          for the PDF files which will be created to hold the contrast
          plots for the 'eset_comb' 'ExpressionSet'. The actually
          filenames will have the name of the contrast appended to this
          stem. 

plotVenn: A boolean specifying whether or not to plot a Venn diagram
          showing the overlap in the most differentially expressed
          probe sets (genes) as identified from the two different
          methods being compared. 

vennFilename: A character string specifying the filename for the PDF
          file which will hold the Venn diagram showing the overlap in
          the most differentially expressed probe sets (genes) as
          identified from the two different methods being compared. 

showTopMatches: A boolean specifying whether or not to show the probe
          sets which are deemed most likely to be differentially
          expressed. 

returnResults: A boolean specifying whether or not to return a list
          containing results generated. 

_V_a_l_u_e:

     The main outputs from this function are a number of PDF files.

     The function only returns results if returnResults=TRUE

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

     Richard D. Pearson

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

     Related methods 'pumaDE' and 'calculateLimma'

