sw                   package:OLIN                   R Documentation

_c_D_N_A _m_i_c_r_o_a_r_r_a_y _d_a_t_a _o_f  _S_W_4_8_0/_S_W_6_2_0 _e_x_p_e_r_i_m_e_n_t

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

     Gene expression in two cancer cell lines, SW480 and SW620, is
     compared.  The SW480 cell line was derived from a colon tumour of
     a 50-year old male patient.  The second cell line (SW620)
     originated from a lymph node metastasis of the same patient. 
     Sharing the same genetic background, these cell lines serve as an
     model of cancer progression.

     Target cDNA from SW480 was labelled with Cy3 whereas cDNA from
     SW620 was labelled with Cy5 using the amino-allyl labelling
     method.  Both cDNA pools were co-hybridised on glass slides with
     8448 spots.  The spots consisted of 3986 distinct
     sequence-verified human cDNA clones (Research Genetics, release
     GF211)  printed in duplicates, 84 spots from non-human cDNA clones
     and a further 154 control spots.  Spots were printed by 4x4 pins.
     The experiment consisted of four replicated arrays derived  from
     separate labelling reactions. Local background spot intensities
     were extracted by QuantArray software (version2.1). Analysis
     showed that replicated spots were highly correlated (average
     Pearson correlation: 0.94).  Since this may interfere with the
     efficiency testing performed (and to reduce the size of the data
     set for illustration purpose), the replicated spots were not
     included here.  Experimental details and further analysis can be
     found in Futschik et al. (2002).

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

     data(sw)

_F_o_r_m_a_t:

     An object of class "marrayRaw"

_S_o_u_r_c_e:

     The data was produced  and  provided by Sharon Pattison of the
     Cancer Genetics lab and Aaron Jeffs of the Otago Genomics facility
     of the University of Otago, Dunedin, New Zealand.

_R_e_f_e_r_e_n_c_e_s:

     M. Futschik, A.Jeffs, S.Pattison, N.Kasabov, M.Sullivan, A.Merrie
     and A.Reeve, Gene expression profiling of metastatic and
     non-metastatic colorectal cancer cell-lines, _Genome Letters_,
     vol.1, No.1, pp. 26-34, 2002

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

     'sw.olin'

