lvs(RG,RA,ref,proportion=0.7,df=3,method=c("joint","rlm"), cov.formula=c("weighted","asymptotic"), spar=NULL,normalize.method=c("vsn","smooth.spline","mixed"), summarize.args=NULL,stratify=TRUE,n.strata=3, level=c("mir","probe"),Atransf=c("sqrt","log"),keep.iset=FALSE,clName, verbose=FALSE,...)
"lvs"(RG,RA,ref,proportion=0.7,df=3,method=c("joint","rlm"), cov.formula=c("weighted","asymptotic"), spar=NULL,normalize.method=c("vsn","smooth.spline","mixed"), summarize.args=NULL,stratify=TRUE,n.strata=3, level=c("mir","probe"),Atransf=c("sqrt","log"), keep.iset=FALSE,clName,verbose=FALSE,...)
"lvs"(RG,RA,ref,proportion=0.7,df=3,method=c("joint","rlm"), cov.formula=c("weighted","asymptotic"), spar=NULL,normalize.method=c("vsn","smooth.spline","mixed"), summarize.args=NULL,stratify=TRUE,n.strata=3, level=c("mir","probe"),Atransf=c("sqrt","log"),keep.iset=FALSE,clName, verbose=FALSE,...)
EList
or RGList
estVC
. If not provided it will
computed (slower),summarize
.estVC
....
FileName
giving the names of the files read, with column Sample
giving the names of the samplse.Background
, Normalization
, is.log
, Summarization
indicate which pre-processing step has been done.lvs
works by first identifying least variant set (LVS) with the smallest array-to-array variation. The total information extracted from probe-level intensity data of all samples is modeled as a function of array and probe effect in order to select the reference set for normalization. If the residual variances and array effects are available, lvs
runs faster because the step of robust linear modeling has already been done. Once the LVS miRNAs are identified, the normalization is performed using VSN
or smooth.spline
.
estVC
, summarize
## Not run:
#
# # Starting from an Elist object called MIR
# data("MIR-spike-in")
# AA <- estVC(MIR,method="joint")
# bb <- lvs(MIR,RA=AA,level="probe")
#
# ##It can also run with object RA missing, but taking longer time
# cc <- lvs(MIR)
# ## End(Not run)
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