Annotation in ExpressionSet object
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NS ▴ 60
@ns-7498
Last seen 2.6 years ago
United States

I have a matrix of gene expression which label of each sample and symbol of each gene is known. I wanna perform gtBroad in globaltest R-package. It needs to convert expression matrix to an ExpressionSet object with known Annotation. How can I do that while I have only the name of genes?

 

EDIT: You can download sample data from this link: https://www.dropbox.com/s/d50tr958yvvcxwx/TEST.Rdata?dl=0

I wanna run the below code:

library(globaltest)
library(GSEABase)
broadset <- getBroadSets(asBroadUri(c('BIOCARTA_HDAC_PATHWAY', 'PID_HDAC_CLASSII_PATHWAY')))
pData <- data.frame(id=resp, row.names=colnames(data))
phenoData <- AnnotatedDataFrame(data=pData)
exprs <- ExpressionSet(data, phenoData=phenoData)
gtBroad (response=id, exprs, id='PID_HDAC_CLASSIII_PATHWAY', collection=broadset)
ExpressionSet globaltest • 1.3k views
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chris86 ▴ 390
@chris86-8408
Last seen 21 months ago
UCL, United Kingdom

Making an expression set object is straight forward. You will need the gene expression data in matrix format with gene names as row names. You will then need an annotation data frame with the sample names as row names (these are column names in the matrix). I have my example below.

data <- as.matrix(data)
row.names(des) <- des$ID
des_ready <- as(des, "AnnotatedDataFrame")
x <- ExpressionSet(data, phenoData=des_ready)

http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/Biobase/html/class.ExpressionSet.html

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Thanks, but it does not solve my problem. I added data and my code to the question. Please take a look at them.

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I think the annotation argument or lack of is the problem, have you tried doing this on the probe expression matrix?

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