ArrayFun

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A package to analyze 2-color expression arrays (cDNA or oligonucleotide) starting with raw (.gpr) data.  This packages makes heavy use of the 'marray' and 'limma' packages from Bioconductor.  The FHm15k and FHm22k data sets are provide array layout information for use with these platforms so you won't need to load GAL files every time you analyze a new set of data. 
    Requires: R>1.80, BioConductor packages: marray, limma, PAMR.
    Source: ArrayFun_0.5.4.tar.gz (right click to download). 
    4.63 MB, MD5 checksum: 3e4cd39f4062e540ef0e6f26516a68f7
    PDF instructions: ArrayFun.pdf
    What it does:

• array.input(): Imports .gpr data into R. Filters control and flagged spots. Creates marrayRaw objects.                 - Choose between a local .gal file or the builtin m22k and m15k layout data to describe the array layout.
  
• array.norm(): Performs loess normalizations and/or scale adjustments. Creates marrayNorm objects.
  
• array.swap(): Inverts the log ratios of samples with dye swaps
• array.avg(): Averages results from sample replicates.
• array.avgGene(): Uses unique gene identifiers (LocusLink) to average together gene replicates within arrays.
• array.trim(): Allows low intensity filters to be applied.
• array.pam(): Uses the PAM algorithm to identify changes in gene expression asssociated with an experimental covariate.    
  

See also:  FHCRC Spotted Array GAL files, GenePix Tips.