| simpleaffy-deprecated {simpleaffy} | R Documentation |
The underlying implementation of simpleaffy has changed significantly
and it now represents QC parameters differently. In particular, it
loads only the QC data for the specified array type. A call to any of these
functions loads the appropriate environment specifed by name.
They therefore been deprecated and WILL disappear
from simpleaffy in the future.
getTao(name) getAlpha1(name) getAlpha2(name) getActin3(name) getActinM(name) getActin5(name) getGapdh3(name) getGapdhM(name) getGapdh5(name) getAllQCProbes(name) getBioB(name) getBioC(name) getBioD(name) getCreX(name) getAllSpikeProbes(name) haveQCParams(name)
name |
The 'clean' CDF name of the array (i.e. the result of calling
cleancdfname on the cdfName
of the AffyBatch object containing the
array data of interest. |
Each of these functions has been replaced by a new function of the
form qc.get.. In order to support ratios other than gapdh and
beta-actin, the appropriate way to get ratios is now to use
qc.get.ratios, which will return a table
containing all suggested ratio calculations for the
array.
Similarly, qc.get.spikes will return a table
containing all spike probesets for the array.
Crispin J Miller
http://bioinformatics.picr.man.ac.uk/
setQCEnvironment
qc
qc.ok
cdfName
cleancdfname
qc.get.ratios
qc.get.spikes
qc.get.probes
#old
getBioB("hgu133plus2cdf")
getActin3("hgu133plus2cdf")
getActinM("hgu133plus2cdf")
getActin5("hgu133plus2cdf")
#new
setQCEnvironment("hgu133plus2cdf")
qc.get.spikes()["bioB"]
r <- qc.get.probes()
r["actin3"]
r["actinM"]
r["actin5"]