diagnoseColRow {biclust} | R Documentation |

Calculate the significance of the discovered patter in the data based on the bootstrapping procedure.

diagnoseColRow(x, bicResult, number, nResamplings, replace = TRUE)

`x` |
data matrix, which |

`bicResult` |
object of class |

`number` |
number of bicluster from the output for the diagnostics |

`nResamplings` |
number of bootstrap replicates |

`replace` |
logical flag for bootstrap (TRUE), or sampling without replacement (FALSE) |

The function computes observed F statistics for row and column effect based on two-way ANOVA model. Bootstrap procedure is used to evaluate the significance of discovered bicluster.
Based on `nResamplings`

replicates, the disribution of F statistics for row and column effects are obtained. The p-value is computed as

*P(A) = F^*(A)_b > F(A)^{obs} /(nResamplings+1)*

Low p-values denote non-random selection of columns for a given bicluster. Large p-values show that in other columns for a given set of genes in the bicluster structure is similar. Hence, bicluster columns were just randomly picked by an algorithm for a set of co-regulated genes.

`bootstrapFstats` |
matrix with two columns, containing values of bootstrap F-statistics. The first column corresponds to row, the second column corresponds to column. |

`observedFstatRow` |
observed F-statistics for the row effect |

`observedFstatCol` |
observed F-statistics for the column effect |

`bootstrapPvalueRow` |
bootstrap p value for row effect |

`bootstrapPvalueCol` |
bootstrap p value for column effect |

Tatsiana KHAMIAKOVA tatsiana.khamiakova@uhasselt.be

`diagnosticTest`

, `diagnosticPlot2`

, `diagnosticPlot`

, `computeObservedFstat`

, `ChiaKaruturi`

#---simulate dataset with 1 bicluster ---# xmat<-matrix(rnorm(50*50,0,0.25),50,50) # background noise only rowSize <- 20 #number of rows in a bicluster colSize <- 10 #number of columns in a bicluster a1<-rnorm(rowSize,1,0.1) #sample row effect from N(0,0.1) #adding a coherent values bicluster: b1<-rnorm((colSize),2,0.25) #sample column effect from N(0,0.05) mu<-0.01 #constant value signal for ( i in 1 : rowSize){ for(j in 1: (colSize)){ xmat[i,j] <- xmat[i,j] + mu + a1[i] + b1[j] } } #--obtain a bicluster by running an algorithm---# plaidmab <- biclust(x=xmat, method=BCPlaid(), cluster="b", fit.model = y ~ m + a+ b, background = TRUE, row.release = 0.6, col.release = 0.7, shuffle = 50, back.fit = 5, max.layers = 1, iter.startup = 100, iter.layer = 100, verbose = TRUE) #Run boosotrap procedure: Bootstrap <- diagnoseColRow(x=xmat, bicResult = plaidmab, number = 1, nResamplings = 999, replace = TRUE) diagnosticPlot(bootstrapOutput = Bootstrap) # plotting distribution of bootstrap replicates

[Package *biclust* version 2.0.3 Index]