For the 1st question, I want to know if I should run a single factor or double factor. These samples are match normal/tumor from different patients so something like this
p1N p1T p2N p2T p3N p3T
do i have to run a double factor run like this:
------------condition---------patientNumber
------------<factor>--------- <factor>
p1N--------normal------------ 1
p1T----------tumor ------------1
p2N---------normal-------------2
p2T----------tumor--------------2
p3N--------normal-------------3
p3T---------tumor--------------3
or a single factor like this:
-------------Condition
-------------<factor>
p1N--------normal
p1T---------tumor
p2N--------normal
p2T---------tumor
p3N--------normal
p3T---------tumor
I suppose the question boils down to whether or not DESeq cares if samples come from different patients.
For the 2nd question, I have a thousand match normal/tumor from the same type of tissue but from different patients, should I run DESeq on all one thousand of them or is it fine to do a smaller amount like one hundred?
p1N p1T p2N p2T p3N p3T
do i have to run a double factor run like this:
------------condition---------patientNumber
------------<factor>--------- <factor>
p1N--------normal------------ 1
p1T----------tumor ------------1
p2N---------normal-------------2
p2T----------tumor--------------2
p3N--------normal-------------3
p3T---------tumor--------------3
or a single factor like this:
-------------Condition
-------------<factor>
p1N--------normal
p1T---------tumor
p2N--------normal
p2T---------tumor
p3N--------normal
p3T---------tumor
I suppose the question boils down to whether or not DESeq cares if samples come from different patients.
For the 2nd question, I have a thousand match normal/tumor from the same type of tissue but from different patients, should I run DESeq on all one thousand of them or is it fine to do a smaller amount like one hundred?
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