I just started a differential expression analysis using DESeq2 with a count dataset. There are two cellines in which I want to detect the DE ; a radiated one and a control one. Now I have used DESeq2 and DESeqDataSetFromMatrix before and they have always worked fine for me, but now for some reason when I want to run DESeqDataSetFromMatrix, the function displays an error message. These are my inputs
head(counts) X01 X02 X03 X04 A1BG 241 48 225 129 A1BG-AS1 46 14 34 45 A1CF 28 5 18 28 A2M 2 0 1 0 A2M-AS1 0 0 0 0 A2ML1 11 1 1 4 head(mycols) #coldata condition = as.factor(c(rep("Ctr",2),rep("Irr",2))) mycols = data.frame(row.names = c("X01","X02","X03","X04"),condition) mycols condition X01 Ctr X02 Ctr X03 Irr X04 Irr >dsd = DESeqDataSetFromMatrix(countData = counts,colData = mycols, design ~ condition)
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData
I don't get error at all, as far as I know, all variables in the design formula (condition here) ARE included as a column in the colData!
I've always done it this way and it's the first time I received this error so I don't know what to do here.
Any help would be greatly appreciated, thanks!!