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Julia Engelmann
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130
@julia-engelmann-559
Last seen 10.2 years ago
Hi list,
I wonder if I can compare Affymetrix arrays of the same type (ATH1)
which were made in different laboratories and with different tissue
types and different references. I have: "tissue1 treated", "tissue1
untreated" from one lab and "tissue2 treated", "tissue2 untreated"
from
the other lab.
The references (untreated) are different because of the different
tissue types. I am interested in the difference between tissue1
treated
and tissue2 treated, so I thought I could use limma to make a
contrast:
(tissue1_treated-tissue1_untreated)-(tissue2_treated-
tissue2_untreated).
I am not sure if this is valid, though? For example, I do not account
for the different labs that way.
Maybe it is just possible to analyse each experiment by itself and
compare the results at a latter stage, say compare lists of
differentially expressed genes?
Any advice, comments or hints are highly appreciated,
Julia