Displaying 2 results from an estimated 2 matches for "meansdplot".
Did you mean:
meanplot
2010 Mar 29
1
stuck with affy / limma
...,hgu133plus2SYMBOL)
heatmap(exprs(x)[sel, ], labRow=u)
### in this case it works to extract the gene symbol
### limma contrasts
design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3)))
colnames(design) <- c("control", "three", "six")
fit <- lmFit(x, design)
meanSdPlot(x)
contrast.matrix <- makeContrasts(three-control, six-control, levels=design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
#### top list
topTable(fit2, coef=1, adjust="BH", number=20, sort.by="M")
library(hgu133plus2.db)
u<-mget(row.names(fit2),h...
2003 May 29
0
Bioconductor 1.2 Released
...accepting input dynamically.
* vsn: vsn can now be used as a normalization method with the affy
package. The likelihood function optimization has been
streamlined and is faster. There is a new function to produce
a diagnostic plot for the variance-mean relationship of
microarray data, meanSdPlot. The data returned by vsn is now
an object of class "exprSet".
* widgetTools: A new package that provides user friendly tools to
create Tcl/Tk widgets in R.
Software, documentation, and further details are available on the
Bioconductor WWW site:
http://www.bioconductor.or...