I have a table of count of control (3 replicates), treatment B (3 replicates) and treatment A (3 replicates). The first column is the gene symbol, table is as below:
Gene_symbol C1 C2 C3 B1 B2 B3 A1 A2 A3
How can I point to DESeq2 that gene symbol isn't row.data ?
Gene_symbol C1 C2 C3 B1 B2 B3 A1 A2 A3
Code:
library( "DESeq2" ) library("Biobase") mydata = read.table("matrix4.txt", header=TRUE) samples <- data.frame(row.names=c("C1", "C2", "C3", "B1", "B2", "B3", "A1", "A2", "A3"), condition=as.factor(c(rep("C",3), rep("B", 3), rep("A", 3)))) dds <- DESeqDataSetFromMatrix(countData = as.matrix(mydata), colData=samples, design=~condition) Error in validObject(.Object) : invalid class “SummarizedExperiment” object: 'colData' nrow differs from 'assays' ncol
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