How to analyze micoarray data with more than one source.

Question

[nanobiotech.com]

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?

Answer 1

[Kevin Blighe]

There was a similar question posted around the same time as yours: Meta-analysis on microaray data, when a sinlge experiment contains diferent tissues

Which tissues are you looking at? Unless you are interested in the cross-tissue differences, then you do not have to process them together.

[nanobiotech.com]

Thank you @kevinBlighe for your reasponse