Fields and Methods
Methods:
rll{
extractDataFrame -
extractMatrix -
readUnits -
}
Methods inherited from AffymetrixCelFile:
[, [[, allocateFromCdf, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributesByTags, setAttributeXY
Methods inherited from GenericDataFile:
getParentName, compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, saveFile format
The idea behind this class is store data fields which by nature have
one value per probe (per field) in CEL files. A perfect example is to
store probe-affinity estimates and their standard deviations. There
is one probe affinity per probe so the structure of a CEL file (and
its coupled CDF file) is well suited to read/write such information.
Consider a unit group with L probes. A CEL file stores
intensities (L floats), stdvs (L floats), and
pixels (L integers). Thus, for each probe l=1,...,L, a
(float, float, integer) tuple is stored. We can use this for any
information we want. If we want a slightly different structure,
we can choose to encode/decode our structure/information to fit the
structure of the CEL file. This abstract class provides transparent
methods for encoding and decoding such information through methods
encodeUnitGroup() and decodeUnitGroup().
By subclassing you can implement different types of data structures.