Use JAMIE
Download and installation
- Click following links to download the package:
- R package source code (can be installed under linux or Mac OSX),
- windows binary package (compiled under R 2.10) for Windows.
- Follow the standard procedure to install the package in your R.
- JAMIE depends on two BioConductor packages affy and affxparser to read and parse BPMAP and CEL files. These are needed for analyzing Affymetrix arrays.
Prepare configuration file
For Affymetrix data the inputs are BPMAP and CEL files. The experiments could be paired (IP and control channels are hybridized from the same biological sample) or non-paired. See example configuration files for paired Affymetrix experiment and non-paired Affymetrix experiment.
For experiments from platform other than Affymetrix, users must prepare a single text file (without column headers) to include all informations. The first two columns need to be chromosome and positions of the probes. From the third column are probe signals (log ratios). See an exmple configuration file for data from other platform.
Use JAMIE
Assume the configuration file is called "config.txt". Running the following two commands in R:
library(jamie)
jamie("config.txt")
The result peak lists will be saved as tab delimited text files in
the working directory user specified.
Examples
This example dataset is from ArrayExpress (accession number E-WMIT-5). The platform is Agilent Human promoter 44k tiling array. There are data for three different transcription factors each with 2 replicates. All data (with tiling array design information) are saved in a single text file.
To try JAMIE, do
- Download data file (27Mb) and configuration file to the same folder.
- Start R and change directory to that folder.
- In R type
library(jamie) jamie("agilent_config.txt")