Question

n of 1 exploratory analysis

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BrainEmpty • 0

@brainempty-24343

Last seen 5.1 years ago

Dear Deseq2 support team, I have set the design~1 to explore 1Ko versus 1WT sample. The results are very sketchy, 80% are significant and none are downregulated, I'm just wondering how can we explore data with n of 1 to see if we go on and sequence more samples? Thank you a lot.

deseq2 • 650 views

ADD COMMENT • link updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by BrainEmpty • 0

score 0 · Answer 1 · 2020-10-12

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Michael Love 43k

@mikelove

Last seen 3 days ago

United States

I don't know what you are doing, you cannot perform DE with 1 vs 1 in DESeq2. The software will give an error.

If you are attempting to do so, I wouldn't trust the results.

ADD COMMENT • link 5.1 years ago Michael Love 43k

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Hi Michael, How would you explore a data with n of 1 without doing DE? Any recommendation?

ADD REPLY • link 5.1 years ago BrainEmpty • 0

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I don't have much advice here, sorry. I rarely encounter experiments where replicates were not performed, as how can one assess the level of technical or biological noise inherent to the data?

ADD REPLY • link 5.1 years ago Michael Love 43k

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Hi Michael, How would you explore a data with n of 1 without doing DE? Any recommendation?

ADD REPLY • link 5.1 years ago BrainEmpty • 0