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Bioconductor Raw Probe Intensity
The users would like to have the raw probe intensities, in a tabular format with one
column of probeset ids, a second column with probe number within that probe set,
and a third column of intensities of the probes.
| What was done | Obtain CEL files:
| 1) | Log in to SBEAMS/Microarray
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| 2) | Choose the 'Project Home' button on the left side of the screen
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| 3) | Choose the 'Data Download' tab along the top of the page
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| 4) | Make sure you have the appropriate project selected in the project
chooser drop-down on the top of the page--you should see your Affy
chips listed on the page
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| 5) | Check the box under CEL for each chip you'd like to analyze
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| 6) | Click the 'GET_AFFY_ARRAY_FILES' button underneath the chip listing, and save these somewhere on your computer.
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| 7) | Unzip the downloaded file to get the actual CEL files.
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| Use R/Bioconductor: | Use the following steps to set up and run R/Bioconductor:
| 1) | R can be downloaded from
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| 2) | Bioconductor packages can be installed by running within R:
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| source("http://www.bioconductor.org/getBioC.R")
getBioC()
| | 3) | Use the following code to load in CEL files, and get the probe intensities in 'Matrix':
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| switch(.Platform$OS.type, unix =
.libPaths("/net/arrays/Affymetrix/bioconductor/library/"),"windows")
library(affy)
# need to substitute in name of directory to which CEL files were saved from SBEAMS
setwd("<font class='highlight'>/path/to/CEL/files</font>")
file.names <- c('20040603_03_LPS1-0.CEL' ,'20040809_03_LPS1-60_4_fold_dilution.CEL',
'20040609_03_LPS1-60.CEL')
data <- read.affybatch(filenames=file.names)
Matrix <- exprs(data)
genes <- geneNames(data)
| | 4) | Grab PM and MM intensities and combine into a matrix of dimensions [3,# probes], output to file:
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| ints <- c( "probe",row.names(pData(data)) )
for( i in 1:length(genes) ) {
int <- pm(data,genenames=genes[i])
tmp <- 1:dim(int)[1]
int.matrix <- as.matrix(int)
row.names(int.matrix) <- rep(genes[i],dim(int.matrix)[1])
tmp <- cbind(tmp,int.matrix)
ints <- rbind(ints,tmp)
}
ints.frame <- as.data.frame(ints)
write.table(ints.frame,paste(output.file.base,"-pm.txt"),sep="\t",col.names=FALSE)
ints <- c( "probe",row.names(pData(data)) )
for( i in 1:length(genes) ) {
int <- pm(data,genenames=genes[i])
tmp <- 1:dim(int)[1]
int.matrix <- as.matrix(int)
row.names(int.matrix) <- rep(genes[i],dim(int.matrix)[1])
tmp <- cbind(tmp,int.matrix)
ints <- rbind(ints,tmp)
}
ints.frame <- as.data.frame(ints)
write.table(ints.frame,paste(output.file.base,"-mm.txt"),sep="\t",col.names=FALSE)
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