npci.index.reconsidered: find targets that have little evidence to be differentially...
In fCI: f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

Description Usage Arguments Details Value Note Author(s) References See Also Examples

the function will be depreciated

1	npci.index.reconsidered(npci.data, expr.by.fold, null.data.start, diff.data.start, gene.indexes, ctr.indexes, trt.indexes, left.fold, right.fold)

`npci.data`	a data frame containing non-zero numeric values (the data frame must contain more than one row and one column)
`expr.by.fold`	a 1xN matrix of case-control fold changes for every gene of the total N genes
`null.data.start`	a Nx1 matrix of control-control fold changes
`diff.data.start`	a Nx1 matrix of case-control fold changes
`gene.indexes`	the genes used for differential expression analysis.
`ctr.indexes`	the control sample column indexes
`trt.indexes`	the case sample column indexes
`left.fold`	the minimum fold changes for downregulation
`right.fold`	the minimum fold changes for upregulation

TBD

values

genes wrongly considered as differentially expressed

TBD

Shaojun Tang

http://software.steenlab.org/fCI/

TBD

  
data.file=data.frame(matrix(sample(3:100, 100*4, replace=TRUE), 100,4))
wt.index=c(1,2)
df.index=c(1,3)
npci=new("NPCI")
npci@wt.index=wt.index
npci@df.index=df.index
npci@sample.data.normalized=data.file
npci=initialize(npci)
npci=normalization(npci)
npci=populate(npci)
npci=compute(npci)
npci=summarize(npci)

npci.data=npci@sample.data.normalized
null.data.start=npci@null.data.start
diff.data.start=npci@diff.data.start
choice=2
rank.index.to.be.removed=npci@rank.index.to.be.removed
expr.by.fold=npci@expr.by.fold

ctr.indexes=1:2
trt.indexes=3:4
use.intersect=FALSE
symmetric.fold=TRUE
fold.cutoff.list=npci@fold.cutoff.list
gene.indexes=npci@diff.gene.ids
left.fold=2
right.fold=2