Question: DESeq2 log2 fold change
7 months ago by
bioinfonerd • 30
bioinfonerd • 30 wrote:
I did the DESeq2 on my Nanostring gene expression data using the below code:
dds <- DESeqDataSetFromMatrix(countData = counts_set,colData = annotation,design = ~ pt_id+treatment) sizeFactors(dds) <- estimateSizeFactorsForMatrix(counts(dds)) dds <- DESeq(dds) res <- results(dds,contrast=c("treatment","Treatment","Vehicle"))
But the log2FC I am getting are quite different from the log2FC I calculated manually. Could you let me know if that is normal and correct?
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