I have simple question concerning replicates and samples.
I have 4 experiment sets that comparing two organs.
Experiment A has:
Organ X - 2 replicates
Organ Y - 2 replicates
Experiment B has
Organ X - 2 replicates
Organ Y - 3 replicates.
Currently in Cuffdiff with False Discovery Rate 0.1, I have set the following sample names:
Experiment A - Organ X with 2 Replicates
Experiment A - Organ Y with 2 Replicates
Experiment B - Organ X with 2 Replicates
Experiment B - Organ Y with 3 Replicates
Is it fine if I do the following:
Organ X - 4 Replicates
Organ Y - 5 Replicates
Is it fine to combine the replicates across the two experiments together and just compare the 2 organs. Currently I am getting good P and Q values.
Thank you in advance.
-Zapages
I have 4 experiment sets that comparing two organs.
Experiment A has:
Organ X - 2 replicates
Organ Y - 2 replicates
Experiment B has
Organ X - 2 replicates
Organ Y - 3 replicates.
Currently in Cuffdiff with False Discovery Rate 0.1, I have set the following sample names:
Experiment A - Organ X with 2 Replicates
Experiment A - Organ Y with 2 Replicates
Experiment B - Organ X with 2 Replicates
Experiment B - Organ Y with 3 Replicates
Is it fine if I do the following:
Organ X - 4 Replicates
Organ Y - 5 Replicates
Is it fine to combine the replicates across the two experiments together and just compare the 2 organs. Currently I am getting good P and Q values.
Thank you in advance.
-Zapages
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