Entering edit mode
9 weeks ago
Larissa
•
0
dds <- DESeqDataSetFromMatrix (countData = countdata,
colData = metadata,
design = ~ Condition + Genotype)
dds <- estimateSizeFactors(dds)
vst_data <- vst(dds, blind = TRUE)
vst_counts <- assay(vst_data)
analysis<- DESeq(vst_counts)
At this step I always have this error:
Error in DESeq(vst_counts) : is(object, "DESeqDataSet") is not TRUE
How to correct that?
As others have said, you should familiarise yourself with the DESeq2 manual, but this is a basic set of commands to doing a DESeq2 analysis.
Provided you've used the right contrast,
dds.res
contains information like LFC, standard error, p-value and adjuvsted p-value for the differentially expressed genes. You can convert it to a data-frame and immediately use it in visualisations like volcano-plots etc.Just remember that DESeq2 will always require raw, untransformed counts for running differential analysis, and the rlog2/vst transformed data for downstream applications.
If you see:
This is skipping the differential expression part and just generates ~log2 transformed data for downstream without doing any statistical testing.