I have received this error:
dataset <- DESeqDataSetFromMatrix(countData = countData, + colData = colData, + design = ~condition) *Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character*
And here is the code I am running :
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESeq2") library('DESeq2') library('RColorBrewer') countFilePath = './count-1.txt' countData = read.table(file = countFilePath, header = FALSE, sep = '\t', row.names = 1,stringsAsFactors=FALSE) ##make first row the colname colnames(countData) <- countData[1,] countData <- countData[-1, ] ##if needed to remove some columes countData = countData[3:ncol(countData)] dim(countData) colFilePath = './colname-Jul12.txt' colData = read.table(file = colFilePath, header = TRUE, sep = ' ', row.names = 1) colData[['condition']] = factor(colData[['condition']], levels = c('Water', '130','160')) colData dataset <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~condition)
Anybody can help me here?
Thank you so much Sali