Displaying 2 results from an estimated 2 matches for "hgu133plus2symbol".
2010 Mar 29
1
stuck with affy / limma
...normalize.param
= list(subsample = 1000), pmcorrect.method = "pmonly", summary.method =
"medianpolish")
### genes with highest variation
library(hgu133plus2.db)
rsd <- apply(exprs(x), 1, sd)
sel <- order(rsd, decreasing = TRUE)[1:250]
u<-mget(row.names(exprs(x)[sel,]),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)
cont...
2012 Apr 03
2
how to map microarray probe to gene, homology
Hi:
I have clustered microarray gene expression data and trying to map between
microarray probe, gene, pathway, gene ontology, and homology for a set of
(affy) microarray probes. Is there any package in R which facilitates this?
I am looking at bioconductor, but till now could not find a solution. A
link to some worked example would be appreciated.
Thanks and regards.
John
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