The following was working just fine last week, however, I keep getting different errors all of a sudden and I don't know why

I've been getting either: duplicate 'row.names' are not allowed

when I delete row.names I get: ncol doesn't equal ncount or I get that there are neg values in my count data, which there are not and I simply can not figure out what's wrong... any suggestions?

I've tried playing around with header and a few other things, but can't figure it out

I think it has something to do with it not correctly reading the first column that has the gene names and the first row that has the names that correspond to who the count values within the matrix belong to, but don't know how to fix it

library("DESeq2")

genecountmatrix <- as.matrix(read.csv("/home/gordovezfa/R/3.5/Shawn/file.csv", row.names = "geneid")) View(genecount_matrix)

RNAseq <- read.csv("/home/gordovezfa/R/3.5/Shawn/file.csv", row.names = "ids") View(SMS_RNAseq)

Disease <- factor(c("SMS","Con"))

genecountmatrix <- as.data.frame(genecountmatrix)

RNAseq <- as.data.frame(RNAseq)

dds <- DESeqDataSetFromMatrix(countData = genecountmatrix, colData = RNAseq, design = ~Disease, tidy = TRUE)

dds

dds <- dds[ rowSums(counts(dds)) > 5,] dds <- DESeq(dds)

res <- results(dds, contrast = c("Disease", "Effec", "Con"), tidy = TRUE) res <- res[order(res$padj),] sum(res$padj < 0.05, na.rm = TRUE)

res <- res[ !is.na(res$padj), ] res <- res[ !is.na(res$pvalue), ] res <- res[, -which(names(res) == "padj")]

sum(res$padj < 0.05)

write.csv(as.data.frame(res), file="SMS.csv")

DESeq2 didn't have any changes that would affect you.

However, you can check yourself for duplicate row names easily enough for x:

any(duplicated(rownames(x)))

There's not a good reason to have duplicated row names during an analysis, they can cause all kinds of confusion.

genecountmatrix <- as.matrix(read.csv("/home/gordovezfa/R/3.5/Shawn/file.csv", row.names = "geneid")) View(genecount_matrix)

RNAseq <- read.csv("/home/gordovezfa/R/3.5/Shawn/file.csv", row.names = "ids") View(SMS_RNAseq)

Are you sure that's right? To be pulling the count data and the sample info data from the file? Your counts should have samples as column names, the other info has sample names as row names.