affycompTable {affycomp} | R Documentation |
These functions takes as an argument the output of the asessment functions.
affycompTable(...,Table=NULL,assessment.list=NULL,method.names=NULL) tableAll(...,assessment.list=NULL,method.names=NULL) tableDilution(l, method.names=NULL) tableFC(l, method.names=NULL) tableFC2(l, method.names=NULL) tableSignal(l, method.names=NULL) tableLS(l, method.names=NULL) tableSpikeInSD(l, method.names=NULL) tableMA2(l, method.names=NULL) tableOverallSNR(...,assessment.list=NULL,method.names=NULL,ngenes=12626) tableRanks(...,assessment.list=NULL,method.names=NULL,ngenes=12626,rank=TRUE)
... |
lists produced by the assessment functions |
Table |
If TableAll was used one can send it through this argument |
assessment.list |
Alternatively, one can also send a list of lists produced by tableAll . |
method.names |
A character vector with the names of the epxression measure methodology. |
l |
list of assessments. |
rank |
if TRUE tableRanks will present ranks instead
of local slopes. |
ngenes |
when computing ranks, out of how many genes should we do it? |
Read the vignette for more details on what the entries of the table
are. affycompTable
has a few entries per graph. tableAll
has more entries. Once an
assessment is used this function knows what to do. You can call any of
the assessment functions described in assessSpikeIn
,
assessDilution
, assessSD
,
assessLS
, assessMA2
, and assessSpikeInSD
.
Note tableRanks
and tableOverallSNR
work on the results
from assessSpikeIn2
.
A matrix. One column per each method and one row for each comparison. tableOverallSNR is an exception. Where rows represnt methods.
Rafael A. Irizarry
data(rma.assessment) ##this was produced with affycomp.assess data(mas5.assessment) ##this one too tmp <- affycompTable(mas5.assessment,rma.assessment) format(tmp,digit=2)