data.raw           package:dyebiasexamples           R Documentation

_E_x_a_m_p_l_e _d_a_t_a _f_o_r _t_h_e _d_y_e_b_i_a_s _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     The 'dyebias'-package, described in Margaritis et al. (2009) can
     be used to get rid of dye bias in two-colour microarrays. The
     'data.raw' and 'data.norm' objects are used in its examples.

     The objects represent four hybridizations of identical mRNA, with
     increasing Cy3 and Cy5 labeling percentages (identical per slide)
     and differently spiked-in external controls to judge the process
     of dyebias correction.

_U_s_a_g_e:

            data(data.raw)
            data(data.norm)

_F_o_r_m_a_t:

     The data uses the 'marray'-package by Dudoit and Yang (2002).
     'data.raw' is a 'marrayRaw' object, 'data.norm' is a 'marrayNorm'
     object derived from it by print-tip LOESS normalization. Neither
     is dyebias-corrected yet.

_D_e_t_a_i_l_s:

     The column 'R.group' of 'maInfo(maTargets(data.norm))' shows the
     details. Eg.,  '4%_2EC' indicates that the labeling (of both
     channels) was at 4%, and the external controls were spiked in at a
     concentration twice that of the green channel. See Margaritis
     et~al. (2009) for details.

_N_o_t_e:

     The Tuteja data is also included in this package under the
     (inst)/doc directory, as this data is not proper rda, tab or csv
     data. For details, refer to the original publication and/or the
     'dyebias' vignette.

_A_u_t_h_o_r(_s):

     Philip Lijnzaad

_S_o_u_r_c_e:

     All accession numbers below refer to ArrayExpress
     (http://www.ebi.ac.uk/microarray).

     This two-colour microarrray data was obtained from identical mRNA
     extracts (protocol P-UMCU-37), spiked with external controls,
     dUTP-labeled with Cy3 and Cy5 (protocol P-UMCU-38). This was
     hybridized (protocol P-UMCU-39) onto self-spotted slides
     containing 70-mer oligonucleotides (2 replicates per oligo, Operon
     "Array-Ready", and including 2838 control features; protocol
     P-UMCU-34).  Scanning was done with an Agilent G2565AA scanner
     (protocol P-UMCU-40) and images were quantified with
     BioDiscovery's ImaGene 7.x (protocol P-UMCU-42)

_R_e_f_e_r_e_n_c_e_s:

     Margaritis, T., Lijnzaad, P., van~Leenen, D., Bouwmeester, D.,
     Kemmeren, P., van~Hooff, S.R and Holstege, F.C.P. (2009).
     Adaptable gene-specific dye bias correction for two-channel DNA
     microarrays. _Molecular Systems Biology, submitted_

     Dudoit, S. and Yang, Y.H. (2002)  Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data.
     In: Parmigiani, G., Garrett, E.S. , Irizarry, R.A., and Zeger,
     S.L. (eds.) _The Analysis of Gene Expression Data: Methods and
     Software_, New~York: Springer

_E_x_a_m_p_l_e_s:

       data(data.raw)
       data(data.norm)

