[BioC] comparing different experiments
julia.engelmann at biozentrum.uni-wuerzburg.de
Tue Nov 9 16:30:53 CET 2004
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:
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,
More information about the Bioconductor