summarize {LVSmiRNA} | R Documentation |
Summarize microRNA microarray data objects.
summarize(object, ...) ## S3 method for class 'EList' summarize(object,RA,remove.ctrl=FALSE,is.log=!is.null(object$preprocessing$Normalization), method=c("rlm","medianpolish","mean"),verbose=FALSE,make.exprs=FALSE,...) ## S3 method for class 'RGList' summarize(object,RA,remove.ctrl=FALSE,is.log=!is.null(object$preprocessing$Normalization), method=c("rlm","medianpolish","mean"),verbose=FALSE,make.exprs=FALSE,...)
object |
an object for which a summary is desired. |
RA |
an object from estVC. |
remove.ctrl |
logical, indicating whether to remove control probes. |
is.log |
Are data already logged? |
method |
currently, method "medianpolish","mean" and "rlm" are supported. |
verbose |
More output |
make.exprs |
Should the output be and |
... |
... |
For multi-probe, multi-replicate microarray, intensities need to be summarized into a single expression value for each miRNA. The data objects are summarized as if they were lists.
An Elist object containing components as follows:
G |
matrix containing the summarized intensities for each array with miRNAs as rows and arrays as columns. |
Gb |
matrix containing the background intensities for each array with probes as rows and arrays as columns. |
targets |
data frame with column |
genes |
data frame containing annotation information about the probes, for examples gene names and IDs and positions on the array. |
source |
character string giving the image analysis program name. |
preprocessing |
list with components |
Stefano Calza <stefano.calza@biostatistics.it>, Suo Chen and Yudi Pawitan.
Irizarry et al., 'Exploration, normalization, and summaries of high density oligonucleotide array probe level data', (2003a, Biostatistics); Huber, P. J., 'Robust estimation of a location parameter', (1964, Annuas of Mathematical Statistics)
## Not run: data("MIR-spike-in") AA <- estVC(MIR,method="joint") dd <- summarize(MIR,RA=AA,method="rlm") ##summarization methods other than rlm, object RA is not required dd1 <- summarize(MIR,method="medianpolish") dd2 <- summarize(MIR,method="mean") ## End(Not run)