DESeq2 log2 fold change
Hi everyone,
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?
Thanks!
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bioinfonerd •
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Every now and then this question appears here:
Discrepancy in DESeq2 fold change
How to recover treated/control count from DESeq2 output
Why can't I replicate DESeq's Log2FC calculation?
I guess that your FCs for the genes with smaller couts are much larger than the DESeq2-ones?
EDIT: You should have a look at this post from the DESeq2 developer towards DESeq2 on Nanostring data. He is concerned that the normalization might be a problem.