ALL                   package:ALL                   R Documentation

_A_c_u_t_e _L_y_m_p_h_o_b_l_a_s_t_i_c _L_e_u_k_e_m_i_a _D_a_t_a _f_r_o_m _t_h_e _R_i_t_z _L_a_b_o_r_a_t_o_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     The data consist of microarrays from 128 different individuals
     with  acute lymphoblastic leukemia (ALL). A number of additional
     covariates are available. The data have been normalized (using
     rma) and it is the jointly normalized data that are available
     here. The data are presented in the form of an 'exprSet' object.

_U_s_a_g_e:

     data(ALL)

_F_o_r_m_a_t:

     The different covariates are:

        *  'cod': The patient IDs.

        *  'diagnosis' The date of diagnosis.

        *  'sex'   The sex of the patient, coded as 'M' and 'F'.

        *  'age'  The age of the patient in years.

        *  'BT'  The type and stage of the disease; 'B' indicates 
           B-cell ALL while a 'T' indicates T-cell ALL. 

        *  'remission' A factor with two levels, either 'CR' indicate 
           that remission was achieved or 'REF' indicating that the
           patient was refractory and remission was not achieved. 

        *  'CR'  A vector with the following values: 1: "CR", remission
           achieved; 2: "DEATH IN CR", patient died while in remission;
           3: "DEATH IN INDUCTION", patient died while in induction
           therapy; 4: "REF", patient was refractory to therapy. 

        *  'date.cr' The date on which remission was achieved.

        *  't(4;11)'  A logical vector indicating whether a t(4;11) 
           translocation was detected.

        *  't(9;22)'  A logical vector indicating whether a t(9;22) 
           translocation was detected.

        *  'cyto.normal' A logical vector indicating whether the 
           cytogenetics were normal.

        *  'citog'  A vector indicating the various cytogenetic
           abnormalities that were detected.

        *  'mol.biol' The assigned molecular biology of the cancer
           (mainly  for those with B-cell ALL), BCR\/ABL, ALL\/AF4,
           E2APBX etc. 

        *  'fusion protein' For those with BCR\/ABL which of the fusion
            proteins was detected,  'p190', 'p190\/p210', 'p210'.

        *  'mdr'   The patients response to multidrug resistance,
           either 'NEG', or 'POS'.

        *  'kinet'  ploidy, either diploid or hyperd.

        *  'ccr'  A vector indicating whether the patient had
           continuous complete remission nor not. 

        *  'relapse'  A vector indicating whether the patient had
           relapse or not.

        *  'transplant'  Did the patient receive a bone marrow
           transplant or not.

        *  'f.u' Follow-up data. The possible values are 1: "AUBMT \/
           REL": autologous bone marrow transplant and subsequent
           relapse; 2: "BMT \/ CCR": allogeneic bone marrow transplant
           and  still in continuous complete remission; 3: "BMT \/
           DEATH IN CR": after allogeneic bone marrow transplant
           patient died without relapsing; 4: "BMT \/ REL": after
           allogeneic bone marrow transplant patient relapsed; 5:
           "CCR": patient was in  continuous complete remission;  6:
           "CCR \/ OFF": patient was in  continuous complete remission
           but off-protocol for some reasons;   7: "DEATH IN CR": died
           when in complete remission; 8: "MUD \/ DEATH IN CR":
           unrelated allogeneic bone marrow transplant and  death
           without relapsing; 9:  "REL": relapse; 10:  "REL \/ SNC":
           relapse occurred at central nervous system.   

        *  { date last seen} Date the patient was last seen.

_S_o_u_r_c_e:

     Sabina Chiaretti, Xiaochun Li, Robert Gentleman, Antonella Vitale,
     Marco Vignetti, Franco Mandelli, Jerome Ritz, and Robin Foa Gene
     expression profile of adult T-cell acute lymphocytic leukemia
     identifies distinct subsets of patients with different response to
     therapy and survival. Blood, 1 April 2004, Vol. 103, No. 7.

_E_x_a_m_p_l_e_s:

     data(ALL)

