Question

Complex DESeq2 Experimental Design

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Elizabeth • 0

@620fb2bd

Last seen 9 months ago

Taiwan

Hi Everyone! I wanted to ask a question regarding the correct method for comparing two sample types that have different controls.

Condition	Treatment Time (0mins)	Treatment Time (20mins)	Treatment Time (120mins)
A	A:0mins	A:20mins	A:120mins
B	B:0mins	B:20mins	B:120mins
C	C:0mins	C:20mins	C:120mins

In essence within DESeq2, I want to get the results of C:120vsC0mins against B20minsvsB0mins.

Has anyone performed this previously? If so, how did you relevel, form new factors and specify the results?

Cheers in advance

DESEq2 DESeq2 • 314 views

ADD COMMENT • link updated 9 months ago by James W. MacDonald 65k • written 9 months ago by Elizabeth • 0

score 0 · Answer 1 · 2023-07-12

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Michael Love 41k

@mikelove

Last seen 8 hours ago

United States

For questions about statistical analysis plan I recommend to work with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site for software related questions.

ADD COMMENT • link 9 months ago Michael Love 41k

score 0 · Answer 2 · 2023-07-12

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 8 hours ago

United States

That's just an interaction. Combine the factor combinations and make the comparisons.

ADD COMMENT • link 9 months ago James W. MacDonald 65k