allQC                  package:mdqc                  R Documentation

_Q_C _r_e_p_o_r_t _f_o_r _M_L_L._B

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

     A subset of arrays from a large acute lymphoblastic leukemia (ALL)
     study

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

     data(allQC)

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

     A data frame with 20 observations on the following 11 variables.

     '_S_c_a_l_e _F_a_c_t_o_r' a numeric vector

     '_P_e_r_c_e_n_t _P_r_e_s_e_n_t' a numeric vector

     '_A_v_e_r_a_g_e _B_a_c_k_g_r_o_u_n_d' a numeric vector

     '_M_i_n_i_m_u_m _B_a_c_k_g_r_o_u_n_d' a numeric vector

     '_M_a_x_i_m_u_m _B_a_c_k_g_r_o_u_n_d' a numeric vector

     '_B_i_o_B' a numeric vector

     '_B_i_o_C' a numeric vector

     '_B_i_o_D' a numeric vector

     '_C_r_e_X' a numeric vector

     '_A_F_F_X-_H_S_A_C_0_7/_X_0_0_3_5_1._3'/_5'' a numeric vector

     '_A_F_F_X-_H_U_M_G_A_P_D_H/_M_3_3_1_9_7._3'/_5'' a numeric vector

_D_e_t_a_i_l_s:

     Contains the QC report obtained using Bioconductor's simpleaffy
     package for a subset of arrays from a large acute lymphoblastic
     leukemia (ALL) study (Ross et al., 2004). The QC report in allQC
     has been generated using the following R commands:


         library("affy")

         ## Get the raw data (see help("MLL.B") for further details)
         library("ALLMLL")
         data(MLL.B)

         ## Generate the QC metrics
         library("simpleaffy")
         data.all <- MLL.B[,1:20]
         all.qc <- qc(data.all)

         ## Select relevant information
         allQC <- cbind(sfs(all.qc),percent.present(all.qc)/100,
                        avbg(all.qc),minbg(all.qc),maxbg(all.qc),
                        spikeInProbes(all.qc),ratios(all.qc)[,c(1,3)])

         ## Specify row and column names                
         colnames(allQC) <- c("Scale Factor","Percent Present", 
             "Average Background", "Minimum Background", "Maximum
     Background", 
             "BioB", "BioC", "BioD", "CreX",
     "AFFX-HSAC07/X00351.3'/5'", 
             "AFFX-HUMGAPDH/M33197.3'/5'")
         rownames(allQC) <- 1:20

     Versions 1.16.0 of affy, 1.2.2 of ALLMLL, and 2.14.05 of
     simpleaffy was used.  Part of this dataset has been also studied
     by Bolstad et al. (2005) and Brettschneider et al. (2007).

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

     Ross, M. E. and Zhou, X. and Song, G. and Shurtleff, S. A. and
     Girtman, K. and Williams, W. K. and Liu, H. and Mahfouz, R. and
     Raimondi, S. C. and Lenny, N. and Patel, A. and Downing, J. R.
     (2003) Classification of pediatric acute lymphoblastic leukemia
     by gene expression profiling. _Blood_ *102*, 2951-9.

     All CEL files are freely available in <URL:
     http://www.stjuderesearch.org/data/ALL3/rawFiles.html.>

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

     Bolstad, B. M. and Collin, F. and Brettschneider, J. and Simpson,
     K. and Cope, L. and Irizarry R. A. and Speed T. P. (2005) Quality
     assessment of Affymetrix GeneChip data. In Gentleman, R. and
     Carey, C. J. and Huber, W. and Irizarry, R. A. and Dudoit, S.
     _Bioinformatics and Computational Biology Solutions Using R and
     Bioconductor._ New York: Springer.

     Brettschneider, J. and Collin, F. and Bolstad, B. M. and Speed, T.
     P. (2007) Quality assessment for short oligonucleotide arrays.
     Forthcoming in _Technometrics (with Discussion)_.

_E_x_a_m_p_l_e_s:

     data(allQC)

