A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations
Example of sequencing data to test the rankReads function.
Calculation of the sorted rank matrix from the dataset
Calculation of the sorted rank matrix from the dataset
Using a C code for merging chromosome segments
Plot a chromosome data
Plot a chromosome segmentation results
Segmentation of a chromosome data
Summarization of the detection results for a list of chromosomes
Calculation of fold change using pairwise comparison values
A Method to Search for Differentially Expressed Genes and to Detect Re...
Search for differentially expressed genes/probes
Search for differentially expressed genes/probes
Calculation of a matrix of fold changes using pairwise comparisons
Search for differentially expressed genes or to detect recurrent copy ...
Read a tab delimited text file
Search for the top N changed genes or probes
Student t-test for detecting differentially expressed genes
Writing the fcros() or pfco() results in a tab delimited text file
Search for the top N changed genes or probes using f-values
Performs a volcano plot of the FCROS/PFCO statistics
Histogram plot function of the fcros package results
Calculation of the mean and the standard deviation of the full or redu...
Searching for differentially expressed genes/probes using an approach ...
Searching for differentially expressed genes or detecting recurrent co...
Search for the top N changed genes or probes using p-values
Performs a volcano plot of the FCROS/PFCO statistics
This function computes a score to assess the significance of sequencin...
Calculation of the FC matrix using pairwise comparisons
Calculation of the reduced matrix containing sorted rank values
Determine numerically a threshold for the ranking score
Performs a total count normalization of reads
Calculation of the Student one sample test probabilities
Compute variance of a beta distribution from data
Transformation of read count values
A fold change rank based method is presented to search for genes with changing expression and to detect recurrent chromosomal copy number aberrations. This method may be useful for high-throughput biological data (micro-array, sequencing, ...). Probabilities are associated with genes or probes in the data set and there is no problem of multiple tests when using this method. For array-based comparative genomic hybridization data, segmentation results are obtained by merging the significant probes detected.