Question: Error in match.arg in boxplot - oligo package
0
gravatar for salamandra
23 months ago by
salamandra180
salamandra180 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 • 867 views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 23 months ago by salamandra180

and how can we solve the error?

ADD REPLYlink written 23 months ago by salamandra180
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1070 users visited in the last hour