While perfroming DEsEq2 analysis, I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedIntegerList"’
Also, I updated all the packages to latest ones inclusing bioconductor.
My code:
Load necessary packages
library(NOISeq)
library(edgeR)
library(DESeq2)
library(ggplot2)
library(reshape2)
library(gplots)
library(RColorBrewer)
library(limma)
library(sva)
library(biomaRt)
library(Rsamtools)
Load Phenotype and count data
rawCountTable <- as.matrix(read.delim(file.choose(), row.names=1))
Col_data = read.table(file = "tLUSC_Phenotype.txt", header = T, sep = "\t")
Run DeSeq2
dds = DESeqDataSetFromMatrix(countData = rawCountTable, colData = Col_data, design = ~ Type)
dds = DESeq(dds)
keep <- rowSums(counts(dds)) >= 10
dds <- dds[keep,]
dds = estimateSizeFactors(dds)
sizeFactors(dds)
vsd <- vst(dds)
vsd2 <- assay(vst(dds, blind=FALSE))
At which step does that come up?
I get this error at the step
Rest all works fine till