test                 package:applera                 R Documentation

_A_n _a_p_p_l_e_r_a _o_b_j_e_c_t _c_o_n_t_a_i_n_i_n_g _3 _c_t_r_l _m_o_u_s_e _a_r_r_a_y_s _a_n_d _t_h_r_e_e _t_r_t _m_o_u_s_e _a_r_r_a_y_s

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

     This dataset is used to test the functionalities of the applera
     package

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

     data(test)

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

     An appleraSet object

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

     Raffaele A. Calogero lab. <raffaele.calogero@unito.it>

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

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

         data(test)
         #brief description of the appleraSet 
         test
         #available slots
         slotNames(test)
         #accessing to the Organism
         organism(test)
         #accessing to the Geneid
         #geneid(test)
         #accessing to the Signal values
        # exprs(signal(test)[1:2,])
         #phenoData associated to the Signal slot
        # pData(signal(test))
         #histograms of the slots of appleraSet
        # hist(test)
         #boxplot of the slots of appleraSet
        # boxplot(test)
         #mva.pairs plot of the wk15
        # samples<-sampleNames(signal(test))[which(signal(test)$wk==15)]
        # mvaAp(subExp(test, samples))
         #subsetting genes by geneNames
        # tmp<-geneNames(signal(test))[1:5]
        # tmp.1<-subGenes(test, tmp)
         #performing loess normalization for the appleraSet
        # test.norm<-normLoess(test)
         #Filtering by signal/noise, keep genes where at least 50
        # sn.subset <- apFilter(test, 0.5, 3, "sn")
         #Filtering by signal/noise, keep genes where at least 50
        # flags.subset <- apFilter(test, 0.5, 2, "flags")
         #Filtering by IQR, 
        # iqr.sn.subset<-iqrFilter(sn.subset, 0.25)    

