Hello! After running DESeq, I attempted to see the results and the following is returned:
results(dds) Error in results(dds) : couldn't find results. you should first run DESeq()
This is right after successfully (I think) running DESeq.
data<-read.csv("TotalRNA_reads.csv", header=TRUE, row.names = 1, stringsAsFactors = FALSE) colnames(data) <- substring(colnames(data), 2) colData<-read.csv("TotalRNA_Sample_Coldata.csv",header = TRUE, row.names = 1) #Double check names match up between Sample and data matrix all(rownames(colData)==colnames(data)) dds<-DESeqDataSetFromMatrix(countData = data, colData = colData, design= ~condition) keep <- rowSums(counts(dds)) >= 10 dds <- dds[keep,] #keeps all but 89 genes DESeq(dds)
The DESeq outputs this as it is running:
estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 11650 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing class: DESeqDataSet dim: 20451 192 metadata(1): version assays(5): counts mu cooks replaceCounts replaceCooks rownames(20451): UBC|7316 GUCY2D|3000 ... LZTFL1|54585 CSF3|1440 rowData names(22): baseMean baseVar ... maxCooks replace colnames(192): 649 1132 ... 11921 12010 colData names(4): condition type sizeFactor replaceable
So I believe it ran correctly... has anyone else encountered this issue with the results() function?