made: made: A package for the reproducible analysis of microarray...
In fboulnois/made: Microarray Analysis of Differential Expression

The made package provides tools for the reproducible analysis of oligonucleotide arrays using a simple, clear, and consistent interface.

A user should first specify the options they require and the groups or conditions they want to compare and generate a configuration file using the write.yaml.config function. After this they can run the entire pipeline using the ma.pipeline function or integrate portions of the analysis separately in a larger workflow. The pipeline includes functions such as normalization using ma.normalize, gene level summarization using ma.summarize, and generating a high-quality report using write.report, including quality assessment if desired. Other functions can be used to read and write various files required by the analysis programmatically. Reading the configuration or group file can be accomplished using the functions read.yaml.config and read.group.file respectively, while writing the configuration file can be accomplished using the function write.yaml.config.

For a detailed introduction, see the user's guide: vignette("made-guide") or try out the Affymetrix example: vignette("example-affymetrix").

fboulnois/made documentation built on May 16, 2019, 12:01 p.m.