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

You need to examine countData as swbarnes2 suggests. It is currently a table of character value data, but needs to be numeric data.

One way to avoid this would be to specify header=TRUE when reading in the data, so R recognizes the data as entirely numeric values. Note that read.delim has header=TRUE by default:

https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/read.table

You may want to get some basic R help from bioinformatic collaborators first.