- new S3 generic function avereps() for averaging over irregularly
spaced replicate spots. A method is defined for MAList objects
and a default method intended for matrices.
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma@32117 bc3139a8-67e5-0310-9ffc-ced21a209358
Gordon Smyth authored on 04/06/2008 09:54:23
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@@ -1,6 +1,6 @@ |
| 1 | 1 |
Package: limma |
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-Version: 2.15.6 |
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-Date: 2008/06/01 |
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+Version: 2.15.7 |
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+Date: 2008/06/04 |
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| 4 | 4 |
Title: Linear Models for Microarray Data |
| 5 | 5 |
Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin and Dongseok Choi. |
| 6 | 6 |
Maintainer: Gordon Smyth <[email protected]> |
| ... | ... |
@@ -147,7 +147,50 @@ avedups.MAList <- function(x,ndups=x$printer$ndups,spacing=x$printer$spacing,wei |
| 147 | 147 |
for (a in other) object$other[[a]] <- avedups(object$other[[a]],ndups=ndups,spacing=spacing,weights=weights) |
| 148 | 148 |
y$weights <- avedups(x$weights,ndups=ndups,spacing=spacing) |
| 149 | 149 |
y$genes <- uniquegenelist(x$genes,ndups=ndups,spacing=spacing) |
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- y$printer <- NULL |
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+ y$printer <- NULL |
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+ y |
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+} |
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+ |
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+avereps <- function(x,ID) UseMethod("avereps")
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+# 4 June 2008 |
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+ |
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+avereps.default <- function(x,ID=rownames(x)) |
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+# Average over irregular replicate spots, for matrices or vectors |
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+# Gordon Smyth |
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+# 3 June 2008. |
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+{
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+ if(is.null(x)) return(NULL) |
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+ x <- as.matrix(x) |
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+ nspots <- nrow(x) |
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+ narrays <- ncol(x) |
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+ ID <- as.character(ID) |
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+ iu <- !duplicated(ID) |
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+ if(mode(x)=="character") return(x[iu,,drop=FALSE]) |
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+ u <- ID[iu] |
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+ nprobes <- length(u) |
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+ y <- x[iu,,drop=FALSE] |
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+ for (i in 1:length(u)) y[i,] <- colMeans(x[ID==u[i],,drop=FALSE],na.rm=TRUE) |
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+ y |
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+} |
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+ |
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+avereps.MAList <- function(x,ID=NULL) |
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+# Average over irregular replicate spots for MAList objects |
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+# Gordon Smyth |
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+# 3 June 2008. |
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+{
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+ if(is.null(ID)) {
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+ ID <- x$genes$ID |
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+ if(is.null(ID)) ID <- rownames(x) |
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+ if(is.null(ID)) stop("Cannot find probe IDs")
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+ } |
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+ y <- x |
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+ y$M <- avereps(x$M,ID=ID) |
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+ y$A <- avereps(x$A,ID=ID) |
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+ other <- names(x$other) |
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+ for (a in other) object$other[[a]] <- avereps(object$other[[a]],ID=ID) |
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+ y$weights <- avereps(x$weights,ID=ID) |
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+ y$genes <- x$genes[!duplicated(ID),] |
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+ y$printer <- NULL |
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| 151 | 194 |
y |
| 152 | 195 |
} |
| 153 | 196 |
|
| ... | ... |
@@ -1,3 +1,9 @@ |
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+4 June 2008: limma 2.15.7 |
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+ |
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+- new S3 generic function avereps() for averaging over irregularly |
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+ spaced replicate spots. A method is defined for MAList objects |
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+ and a default method intended for matrices. |
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+ |
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1 June 2008: limma 2.15.6 |
| 2 | 8 |
|
| 3 | 9 |
- gls.series() now preserves rownames (probe IDs) of the expression |
| 4 | 10 |
new file mode 100644 |
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@@ -0,0 +1,34 @@ |
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+\name{avereps}
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+\alias{avereps}
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+\alias{avereps.default}
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+\alias{avereps.MAList}
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+\title{Average Over Irregular Replicate Spots}
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+\description{
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+Condense a microarray data object so that values for within-array replicate spots are replaced with their average. |
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+} |
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+\usage{
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+\method{avereps}{default}(x, ID=rownames(x))
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+\method{avereps}{MAList}(x, ID=NULL)
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+} |
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+\arguments{
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+ \item{x}{a matrix-like object, usually a matrix or an \code{MAList} object.}
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+ \item{ID}{probe identifier.}
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+} |
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+\details{
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+A new data object is computed in which each probe is represented by the average of its replicate spots. |
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+For an \code{MAList} object, the components \code{M} and \code{A} are both averaged in this way, as \code{weights} and any matrices found in \code{object$other}.
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+ |
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+For an \code{MAList} object, \code{ID} defaults to \code{MA$genes$ID} is that exists, otherwise to \code{rownames(MA$M)}.
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+ |
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+If \code{x} is of mode \code{"character"}, then the replicate values are assumed to be equal and the first is taken as the average.
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+} |
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+\value{
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+A data object of the same class as \code{x} with a row for each unique value of \code{ID}.
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+} |
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+\author{Gordon Smyth}
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+\seealso{
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+ \code{\link[base]{dimnames}} in the base package.
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+ |
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+ \link{02.Classes} gives an overview of data classes used in LIMMA.
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+} |
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+\keyword{array}
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