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Each of these functions has been replaced by a new function of the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"]