aroma-project.org

Packages

• Install an aroma.* package
• Update or patch an aroma.* package
• Access the source code

Directories and files

• Access CEL files in a non-standard directory using links
• Use fullname translators to rename data files
• Use fullname translators to rename data sets [VOLUNTEERS NEEDED]

Setting up data sets

• Setting up an AffymetrixCelSet
• Setting up a ChipEffectSet
• Setting up a SnpChipEffectSet or a CnChipEffectSet
• Setting up an AromaUnitTotalCnBinarySet or an AromaUnitFracBCnBinarySet

Subsettings

• Extracting a sub dataset from a data set
• Extracting a single data file from a data set
• Indexing data files by their names
• Indexing data files by a regular expression matching their names

Calculations

• Calculate the average signals of any number of samples
• Calculate total copy number ratios from from total (non-polymorphic) signals

Export signals

• Export total copy numbers and allele B fractions as aroma binary data files [DOC IN PROGRESS]
• Write total copy numbers and allele B fractions as tab-delimited text files [DOC IN PROGRESS]

Extract data as basic R objects

• Extract probeset summaries (chip effects) as a data frame
• Extract probeset summaries (chip effects) as a multi-dimensional array

Extract data as objects recognized by Bioconductor packages

Both probe-level data and probe-summary data can be exported by aroma.* packages for further analysis in Bioconductor.  Note that most of these methods will export data as in-memory object, because that is how most of Bioconductor is designed.  For large probe-level data set this often means that it is not possible not export the complete data set.  For probe-summarized data, an order of magnitude larger data sets can be exported, but for really large data sets working with in-memory object will also become a problem.

• Extract probe signals as an 'affy' AffyBatch object
• Extract probeset summaries (chip effects) as a 'Biobase' ExpressionSet object
• Extract probeset summaries (chip effects) as an 'oligo' SnpQSet or SnpCnvQSet object
• Use aroma.* data within Bioconductor

Interaction with Bioconductor packages

• Use Bioconductor data in aroma.*

Miscellanous

• Migrate and reproduce an analysis elsewhere
• Migrating all or parts of a project to another file system [VOLUNTEERS NEEDED]
• Run CRMA v2 on a subset of arrays in a data set
• Distributed CRMA v2 processing across multiple machines [VOLUNTEERS NEEDED]
• Improve processing time
• Delete intermediate data files while keeping final ones
• Process CEL files with mixed chip type aliases

Building custom-made annotation data

CDF (Chip Definition File)

• Create a CDF file from scratch
• Create a CDF file from an R package/environment
• Create a CDF (and associated) files from a BpMap file (tiling arrays)

Aroma-specific annotation files

• Create a Unit Genome Position (UGP) files
• Create a Unit Fragment Length (UFL) files
• Create an Aroma Cell Sequence (ACS) file
• Write annotation data as a tab-delimited text file

MS Windows specific solutions

• Use filenames longer than 255 characters on Windows