deseq2 RLE normalization
Hi. how can I normalize raw counts using RLE option?
I’ve looked into deseq2 manual, but there’s no information about RLE normalization. It seems it has removed or changed.
Here’s my code below.
Code should be placed in three backticks as shown below.
The codes are reffered from chatgpt.
Thanks for help.
dds <- DESeqDataSetFromMatrix(countData = Counts, colData = coldata, design = ~condition) # Estimate size factors using RLE method dds <- estimateSizeFactors(dds, type="relative") **Error in match.arg(type, c("ratio", "poscounts", "iterate")) : 'arg' should be one of “ratio”, “poscounts”, “iterate”** # Retrieve normalized counts normcounts <- counts(dds, normalized=TRUE)
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