OUTRIDER for gene expression outliers (could not find function "OutriderDataSet")
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Entering edit mode
2.1 years ago

Hi all,

This is my first post on here, and I haven't been able to find any other examples of problems with Outrider so far. I'm still hopeful someone might have the smarts to help me solve this issue.

I'm trying to run my very first OUTRIDER script in RStudio, but I keep getting an error message saying one of the functions cannot be found. Can anyone advise what might be causing this error or what might work to fix it?

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("OUTRIDER")

library(OUTRIDER) browseVignettes("OUTRIDER")

get data

ctsFile <- "OTRDGTEX2.txt"

ctsTable <- read.table(ctsFile, check.names=FALSE) ods <- OutriderDataSet(countData=ctsTable)

filter out non expressed genes

ods <- filterExpression(ods, minCounts=TRUE, filterGenes=TRUE)

run full OUTRIDER pipeline (control, fit model, calculate P-values)

ods <- OUTRIDER(ods)

Console output

ctsFile <- "OTRDGTEX2.txt" ctsTable <- read.table(ctsFile, check.names=FALSE) ods <- OutriderDataSet(countData=ctsTable) Error in OutriderDataSet(countData = ctsTable) : could not find function "OutriderDataSet"

RNA-Seq R sequencing bioconductor • 470 views
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Entering edit mode

Did you get any warnings when loading the OUTRIDER library?

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Entering edit mode
2.1 years ago

I'm not able to remember unfortunately. Instead I installed ran the program through linux and it worked fine. I shall try reinstalling.

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