deseq2 RLE normalization

@55ad8686

Last seen 7 hours ago

South Korea

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.
Best regards,

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)

@atpoint-13662

Last seen 15 hours ago

Germany

Use the function with default settings. That is what RLE is. See the funcrion help to see what the three options mean or just leave at default which is fine most of the time.