Hi every one!
How should one analyze microarray studies that include >1 tissues, such as:
source condition
tis1 dis
tis1 dis
tis1 dis
tis1 ctrl
tis1 ctrl
tis1 ctrl
tis2 dis
tis2 dis
tis2 dis
tis2 ctrl
tis2 ctrl
tis2 ctrl
structure(c("tis1", "tis1", "tis1", "tis1", "tis1", "tis1", "tis2",
"tis2", "tis2", "tis2", "tis2", "tis2", "dis", "dis", "dis",
"ctrl", "ctrl", "ctrl", "dis", "dis", "dis", "ctrl", "ctrl",
"ctrl"), .Dim = c(12L, 2L))
Is it customary to :
'neglect' source column above? OR Do separate analysis for each tissue (and then how to combine DEGs?) OR use features from limma such as blocking (that I am not much acquainted with, requesting help) OR
Do all possible analyses including the 3 just mentioned and select the "best looking" one?
Thank you @kevinBlighe for your reasponse