Question: PGSEA Steps Using Bioconductor
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gravatar for livdiehard
3.7 years ago by
livdiehard0
livdiehard0 wrote:

Hi

Am doing my final year project on a web base application for microarray .
One of my faeture is Gene Set Analysis using the PGSEA technique.
the problem is that am getting confusion with some of the codes.

For Gene Set Analysis, the user has to inputs:

1)CELL Files
2)choose identifier type
3)choose GO
4)choose the pgsea method.

What I actually do is determing in the code below where to pass the identifier and the GO?
Can you help me out?

####code

library(PGSEA)
library(GEOquery)
library(GSEABase)
library(hgu133plus2.db)
gse <- getGEO("GSE7023",GSEMatrix=TRUE)

subtype <- gsub("\\.", "_",gsub("subtype: ", "", phenoData(gse[[1]])$"characteristics_ch1"))
pheno <- new("AnnotatedDataFrame", data = data.frame(subtype), varMetadata = data.frame(labelDescription="subtype"))
rownames(pheno@data) <- colnames(exprs(gse[[1]]))
eset <- new("ExpressionSet", exprs = exprs(gse[[1]]), phenoData = pheno)

data(VAIgsc)
details(VAIgsc[[1]])

pg <- PGSEA(eset, VAIgsc, ref=which(subtype=="NO"))

pg[5:8, 5:8]

range(pg, finite=TRUE)
smcPlot(pg, col=.rwb, scale=c(-15, 15))

microarray pgsea • 587 views
ADD COMMENTlink modified 3.7 years ago by Dan Tenenbaum8.2k • written 3.7 years ago by livdiehard0

Edited your question to add the 'pgsea' tag. This makes it more likely that the maintainer of that package will see your question.

 

ADD REPLYlink written 3.7 years ago by Dan Tenenbaum8.2k
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