I downloaded R 4.1.2 64bit and downloaded DESeq2 in R by if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESeq2") Install information from https://bioconductor.org/packages/release/bioc/html/DESeq2.html My code DESeqDataSetFromMatrix use to work in R-3.1.2. with DESeq2 downloded from biocLite. Now with newer version R and DESeq2, I got the following error. Could anyone help me? It could be I need a different version of DESeq2.
Here is the code - ```r library("DESeq2") file <- read.csv("DMSO_Ana_MeSC_drop.txt", sep="\t",header=TRUE,row.names=1) file[is.na(file)] <- 0 metadata <- read.csv("metadata/metadata_DMSO_Ana_MeSC.txt",sep="\t",header=TRUE,row.names=1)
dds <- DESeqDataSetFromMatrix(countData = file, colData = metadata, design = ~ Condition) ```r
Here is the Error from calling DESeqDataSetFromMatrix sessionInfo( )
Error in SummarizedExperiment(assays = SimpleList(counts = countData), : the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object (or derivative) to construct