Error in match.arg in boxplot - oligo package
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4.3 years ago
salamandra ▴ 410

When running the following code:

library(oligo)
library(GEOquery)
getGEOSuppFiles("GSE38792")
list.files("GSE38792")
untar("GSE38792/GSE38792_RAW.tar", exdir = "GSE38792/CEL")
list.files("GSE38792/CEL")
celfiles <- list.files("GSE38792/CEL", full=T)
celfiles
# read cel files
rawData <- read.celfiles(celfiles)
rawData
boxplot(rawData)

I get this error with boxplot(rawData):

Error in match.arg(target, c("probeset", "core", "full", "extended")) : 'arg' should be one of "probeset", "core", "full", "extended"

However, when running boxplot on normalized data there's no error:

normData <- rma(rawData)
normData
boxplot(normData)

Could someone please tell me why is that?

R oligo • 2.0k views
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and how can we solve the error?

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2.2 years ago
Satyajeet Khare ★ 1.6k

Try

boxplot(rawData, "all", las=3)
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