qua                 package:kidpack                 R Documentation

_r_e_n_a_l _c_e_l_l _c_a_n_c_e_r _r_a_w _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     renal cell cancer raw data

_U_s_a_g_e:

     data(qua)
     data(spotanno)
     data(hybanno)

_F_o_r_m_a_t:

     'qua' is an '8704x4x175' array. Its first dimension are the spots
     (probes) on the arrays, its second dimension are four different
     spot statistics ('fg.green', 'bg.green', 'fg.red', 'bg.red'), its
     third dimension are the 175 different arrays.

     'spotanno' is a data frame with 8704 rows, one for each spot. Its
     columns are: 'Block', 'Row', 'Column', 'AccNumber', 'Name',
     'SrcPlt', 'SrcRow', 'SrcCol', 'vendor',  'ImageID', 'probe'. The
     column 'spotanno$probe' is of class 'numeric', with values from 1
     to 4224, referring to the rows of 'cloneanno'.

     'hybanno' is a data frame with 175 rows, one for each array. Its 
     columns are: 'filename', 'patientid', 'slideid'. The column
     'patientid' is of class 'character', refering to the patients in 
     'pData(eset)'.

_S_o_u_r_c_e:

     Holger Sueltmann, DKFZ. Also available from  ArrayExpress,
     Accession number E-DKFZ-1.

     The data import fro Genepix files and Excel tables, and the
     preprocessing is described in the files preproc.Rnw and
     preproc.pdf in the 'scripts' subdirectory of the package. Please
     refer to these for details!

_R_e_f_e_r_e_n_c_e_s:

     Gene expression in kidney cancer is associated with novel tumor
     subtypes,  cytogenetic abnormalities and metastasis formation.
     Holger Sueltmann, Anja von Heydebreck, Wolfgang Huber, Ruprecht
     Kuner,  Andreas Buness, Markus Vogt, Bastian Gunawan, Martin
     Vingron,  Laszlo Fuezesi, and Annemarie Poustka. Submitted.

_S_e_e _A_l_s_o:

     'eset'

_E_x_a_m_p_l_e_s:

     data(qua)
     qua[1,,1]
     data(spotanno)
     spotanno[1,]
     data(hybanno)
     hybanno[1,]

     ## see also the vignette

