rmaaddon | R Documentation |
Performs RMA with addon quantile normalization by using documentation by value (Kostka & Spang, 2008).
rmaaddon(params, affybatchtest)
params |
object of class |
affybatchtest |
object of class |
This function uses code from the off-CRAN package docval
, version 1.0.
The covariate matrix of the test data after addon normalization. Observations in rows, variables in columns.
Roman Hornung
Kostka, D., Spang, R. (2008). Microarray based diagnosis profits from better documentation of gene expression signatures. PLoS Computational Biology 4(2):e22, <doi: 10.1371/journal.pcbi.0040022>.
## Not run: # Read in example data from ArrayExpress-webpage: library("ArrayExpress") expFiles <- getAE("E-GEOD-62837", path = tempdir(), type = "raw") rawfiles <- file.path(tempdir(), expFiles$rawFiles) library("affy") # Training data: affybatchtrain <- ReadAffy(filenames=rawfiles[1:3]) # Test data: affybatchtest <- ReadAffy(filenames=rawfiles[4:5]) try(file.remove(file.path(tempdir(), expFiles$rawFiles))) try(file.remove(file.path(tempdir(), expFiles$processedFiles))) try(file.remove(file.path(tempdir(), expFiles$sdrf))) try(file.remove(file.path(tempdir(), expFiles$idf))) try(file.remove(file.path(tempdir(), expFiles$adf))) try(file.remove(file.path(tempdir(), expFiles$rawArchive))) try(file.remove(file.path(tempdir(), expFiles$processedArchive))) # RMA normalization with documentation by value: rmaparams <- rmatrain(affybatchtrain) Xtrainnorm <- rmaparams$xnorm dim(Xtrainnorm) # RMA addon normalization: Xtestaddonnorm <- rmaaddon(rmaparams, affybatchtest) dim(Xtestaddonnorm) ## End(Not run)
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