rlog() transformation works only when using DESeqDataSet, not matrix
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licheny • 0
@67db40bc
Last seen 20 days ago
South Korea

When I do transformation a count matrix (matrix datatype was used) by rlog(), it never finished (3 days~). (sample number was only 4~6) But when I used the same contents in the form of DESeqDataSet datatype (by DESeqDataSetFromMatrix(), with design = ~1), it took less than 1 second only.

I saw other cases that claimed too much time spending problem in rlog(). I am worried that it is a kind of bug or something, so I would like to suggest testing this problem.

Thank you.

DESeq2 • 59 views
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@mikelove
Last seen 3 hours ago
United States

Can you make a reproducible example eg with makeExampleDESeqDataSet?

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