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

This error is an important one (it is not from DESeq2 but from SummarizedExperiment): you have provided colnames of the count data, and rownames of the the sample metadata, but these are not the same.

You should examine colnames() of countData and rownames() of colData -- sample swaps at this point can ruin an analysis.

If they are in the wrong order, you need to make sure they are in the same order before providing to DESeq2.

If they are in the same order but named slightly differently, I'd recommend to fix this upstream so each sample has a consistent identifier.