Question: Error in match.arg in boxplot - oligo package
0
gravatar for salamandra
3.9 years ago by
salamandra360
salamandra360 wrote:

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?

oligo R • 1.8k views
ADD COMMENTlink modified 21 months ago by Satyajeet Khare1.6k • written 3.9 years ago by salamandra360

and how can we solve the error?

ADD REPLYlink written 3.9 years ago by salamandra360
0
gravatar for Satyajeet Khare
21 months ago by
Satyajeet Khare1.6k
Pune, India
Satyajeet Khare1.6k wrote:

Try

boxplot(rawData, "all", las=3)
ADD COMMENTlink written 21 months ago by Satyajeet Khare1.6k
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