DESeqDataSet(se, design = design, ignoreRank) 中的错误：计数矩阵应该是数字，当前它具有模式：逻辑

Question

我正在运行对数据集进行 RNA Seq 分析，并且在使用 DESeqDataSetFromMatrix 时不断收到此错误。 df是计数数据，coldata是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)

关于如何改进此代码以使 DESEQ2 运行无误的任何建议？

Answer 1

我不确定您使用的是哪个版本的 R，但您可以做的几件事是：

在上传带有计数的数据框时指示分隔符 (sep=",")
您还可以使用 data.matrix()
彻底检查 DESeq2 插图。 browseVignettes("DESeq2")

DESeqDataSet(se, design = design, ignoreRank) 中的错误：计数矩阵应该是数字，当前它具有模式：逻辑

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

r

count

dataset

rna-seq