Question

DESeq2 using multiple conditions

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aangajala ▴ 20

@aangajala-12237

Last seen 6.9 years ago

Hello, I have multiple conditions, such as condition1( Normal and Cancer), condition2( age bellow 50 and above50), so I want to see DEGs of age in Normal samples and cancer.

So for this do I have produce dds twice by separating coldata , one for normal and one for primary. And then use condition for age ?

Please advice.

Thank you.

deseq2 • 1.1k views

ADD COMMENT • link updated 6.9 years ago by Michael Love 43k • written 6.9 years ago by aangajala ▴ 20

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Sorry...

design(ddsMF) <- formula(~ type + condition)

My question is how many variables can we give. Here in this code only two variables are used? Or is there a limit?

ADD REPLY • link updated 6.9 years ago by Michael Love 43k • written 6.9 years ago by aangajala ▴ 20

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You should look up the “Interactions” section of the vignette, and you can follow the construction of a new variable group using the factor() and paste() functions.

ADD REPLY • link 6.9 years ago Michael Love 43k

score 1 · Answer 1 · 2018-02-12

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Entering edit mode

Michael Love 43k

@mikelove

Last seen 3 days ago

United States

Hi,

Please look over the detailed vignette, A lot of your questions can be answered there:

vignette(“DESeq2”)

ADD COMMENT • link 6.9 years ago Michael Love 43k