deseq2 RLE normalization
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SH • 0
@55ad8686
Last seen 8 weeks 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)
RLE normalization deseq2 • 826 views
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ATpoint ★ 3.9k
@atpoint-13662
Last seen 10 minutes 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.

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