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Question: DESeq2 using multiple conditions
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gravatar for aangajala
9 days ago by
aangajala0
aangajala0 wrote:

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.

ADD COMMENTlink modified 9 days ago by Michael Love16k • written 9 days ago by aangajala0

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 REPLYlink modified 9 days ago by Michael Love16k • written 9 days ago by aangajala0
1

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 REPLYlink written 9 days ago by Michael Love16k
1
gravatar for Michael Love
9 days ago by
Michael Love16k
United States
Michael Love16k wrote:

Hi,

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

vignette(“DESeq2”)

ADD COMMENTlink written 9 days ago by Michael Love16k
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