fcros - A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

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.

Last updated 6 years ago

2.37 score 39 scripts 485 downloads

madsim - A Flexible Microarray Data Simulation Model

This function allows to generate two biological conditions synthetic microarray dataset which has similar behavior to those currently observed with common platforms. User provides a subset of parameters. Available default parameters settings can be modified.

Last updated 8 years ago

1.30 score 2 stars 10 scripts 184 downloads

psvd - Eigendecomposition, Singular-Values and the Power Method

For a data matrix with m rows and n columns (m>=n), the power method is used to compute, simultaneously, the eigendecomposition of a square symmetric matrix. This result is used to obtain the singular value decomposition (SVD) and the principal component analysis (PCA) results. Compared to the classical SVD method, the first r singular values can be computed.

Last updated 5 months ago

1.00 score 523 downloads