Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical

Question

I am running RNA Seq analysis on a dataset and I keep receiving this error when using DESeqDataSetFromMatrix. The df is counts data and the coldata is coldata.

Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical Here is the code being used:

    df <- "C:\\Users\\reach\\OneDrive\\Desktop\\REU Summer 2021\\Autotaxin Cancer\\mRNA_counts_and_annotation\\mRNA_counts.csv"
    df <- read.csv(df)
    coldata <- "C:\\Users\\reach\\OneDrive\\Desktop\\REU Summer 2021\\Autotaxin Cancer\\mRNA_counts_and_annotation\\coldata.txt"
    coldata <- read.csv(coldata)

    coldata <- coldata %>%
      dplyr:: filter("condition" == "Tumor"| "condition" == "Normal" | "condition" == "At_risk")
    coldata %>% select(condition)
    colnames(df) <- stringr::str_replace_all(string = colnames(df),pattern = "-", replacement = "_")
    geneID <- rownames(df)
    df <- df%>%
    dplyr::select(rownames(coldata))

    coldata$condition <- as.factor(coldata$condition)
    df <- df[,rownames(coldata)]
    all(rownames(coldata) %in% colnames(df))
    all(rownames(coldata) == colnames(df))
    ddsall <- DESeq2::DESeqDataSetFromMatrix(countData = df,
                                  colData = coldata,
                                  design = ~ condition)

Any suggestions on how to improve this code so that the DESEQ2 runs without error?

Answer 1

I am not sure which version of R you use but a couple of things you can do is:

1. to indicate the separator (sep=",") when uploading your data frame with counts
2. you can also convert a data frame to numeric matrix using data.matrix()
3. go through DESeq2 vignette thoroughly. browseVignettes("DESeq2")