Tools and Protocols

* CD_Atdschipb520654_rev1.zip, a collection of library files needed for the GeneChip® Command Console® Software (AGCC) to process the AGRONOMICS1 arrays.

* The following CDF files contain the probe set names and the list of associated features (X/Y feature coordinate on the array and other attributes) for each probe set:

agronomics1_allprobes.cdf	CDF for RMA, all genes (TAIR8)
agronomics1_ath1probes.cdf	CDF for RMA, ATH1 probes only (TAIR8)
agronomics1_ath1.cdf	CDF for RMA, ATH1 probes only (TIGR2)
agronomics1_cntrl.cdf	CDF for RMA, a set of random probe sets
agronomics1_tair9_exon.cdf	CDF for RMA, all exons (TAIR9)
agronomics1_tair9_gene.cdf	CDF for RMA, all genes (TAIR9)

* The BP map (Binary Probe Map) file contains the genomic probe position map. The BPMAP file maps the X/Y coordinate of a probe on a GeneChip array to a genomic position for an intended function (agronomics1F-3.bpmap).

* Text version of probe sets per genes (agronomics1_probeseq.txt.gz).

* R script files:

agronomicsTools01.r	R script, functions for RMA-type analysis
example_agronomics1_rma.r	R script, example for RMA-type analysis

The first script defines various functions to perform RMA analysis. Two functions are relevant for the user: aromaRMA and AGRONOMICS1_RMA. Both functions require the aroma.affymetrix package and its special directory structure to organize raw and processed data. aromaRMA is a generic wrapper to make RMA analysis of any Affymetrix array with any matching CDF file easy (note that improved CDF files can for instance be found here). AGRONOMICS1_RMA is a wrapper to perform RMA analysis specifically with AGRONOMICS1 arrays. This function includes the probe filtering algorithm described in our publication. The second script demonstrates how to use the aromaRMA and AGRONOMICS1_RMA functions.

*Example data:

exampleData.zip

example CEL files and instructions to set up a directory structure for the aroma R package

Unzip the file into a local directory, open the file createDirectoryStructure.r, define the path to the unzipped example files and the path to the desired home directory for aroma and run the modified script in R. The script will create the directory structure needed for aroma, it will copy script files, example CEL files and commonly used CDF files into the appropriate subdirectories.

* Files for Model-based Analysis of Tiling-arrays (MAT):

agronomics1_ath.nr.bpmap	MAT-style BPMAT file
agronomics1_mat.acm	ACM file
agronomics1_mat.acs	ACM file
agronomics1_mat.cdf	CDF for MAT

MAT is an alternative to Affymetrix' Tiling Array Software (TAS) to analyze ChIP-chip data. The MAT-style BPMAP file (note the TAIR8-based chromosomal coordinates!) is required for any MAT implementation. The ACM, ACS and CDF files are in addition required for the MAT implementation in aroma.affymetrix. Results generated with either TAS or MAT can be visualized with genome browsers such as the Integrated Genome Browser (IGB).

* Paper describing the AGRONOMICS1 Tiling array (Rehrauer et al., AGRONOMICS1 - A new resource for Arabidopsis transcriptome profiling. Plant Physiology PMID: 20032078).

* The Standard Operating Procedure contains information about:
- Total RNA extraction and quality control
- Microarray target preparation
- Array hybridization
- Normalization and generation of probe set summaries

Please, note that most of the files have been compressed using 7-Zip or WinZip.

 

Update (07/09/2010)

AGRONOMICS consortium will no longer provide new CDF files. For future genome versions, we recommend to use this publicly available microarray facility that contains regularly curated CDF files for Affy-based arrays based on the latest genome annotation.

 

Update (03/09/2012)

New files for AGRONOMICS1 tiling arrays were released. (Reference, download)

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