swirl             package:marrayClasses             R Documentation

_G_e_n_e _e_x_p_r_e_s_s_i_o_n _d_a_t_a _f_r_o_m _S_w_i_r_l _z_e_b_r_a_f_i_s_h _c_D_N_A _m_i_c_r_o_a_r_r_a_y _e_x_p_e_r_i_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     The 'swirlRaw' dataset consists of an object 'swirl' of class
     '"marrayRaw"', which represents pre-normalization intensity data
     for a batch of cDNA microarrays.  

     This experiment was carried out using zebrafish as a model
     organism to study early development in vertebrates. Swirl is a
     point mutant in the BMP2 gene that affects the dorsal/ventral body
     axis. Ventral fates such as blood are reduced, whereas dorsal
     structures such as somites and notochord are expanded. A goal of
     the Swirl experiment is to identify genes with altered expression
     in the swirl mutant compared to wild-type zebrafish. Two sets of
     dye-swap experiments were performed, for a total of four replicate
     hybridizations. For each of these hybridizations, target cDNA from
     the swirl mutant was labeled using one of the Cy3 or Cy5 dyes and
     the target cDNA wild-type mutant was labeled using the other dye.
     Target cDNA was hybridized to microarrays containing 8,448 cDNA
     probes, including 768 controls spots (e.g. negative, positive, and
     normalization controls spots). Microarrays were printed using 4
     times 4 print-tips and are thus partitioned into a 4 times 4 grid
     matrix. Each grid consists of a 22 times 24 spot matrix that was
     printed with a single print-tip. Here, spot row and plate
     coordinates should coincide, as each row of spots corresponds to
     probe sequences from the same 384 well-plate.

     Each of the four hybridizations produced a pair of 16-bit images,
     which were processed using the image analysis software package
     'Spot'. Raw images of the Cy3 and Cy5 fluorescence intensities for
     all fourhybridizations are available at <URL:
     http://fgl.lsa.berkeley.edu/Swirl/index.html>.the dataset includes
     four output files 'swirl.1.spot', 'swirl.2.spot', 'swirl.3.spot',
     and 'swirl.4.spot' from the 'Spot' package.  Each of these files
     contains 8,448 rows and 30 columns; rows correspond to spots and
     columns to different statistics from the 'Spot' image analysis
     output. The file 'fish.gal' is a gal file generated by the
     'GenePix' program; it contains information on individual probe
     sequences, such as gene names, spot ID, spot coordinates. 
     Hybridization information for the mutant and wild-type target
     samples is stored in 'SwirlSample.txt'.

_U_s_a_g_e:

     data(swirl)

_S_o_u_r_c_e:

     These data were provided by Katrin Wuennenberg-Stapleton from the
     Ngai Lab at UC Berkeley. The swirl embryos for this experiment
     were provided by David Kimelman and David Raible at the University
     of Washington.

