[BioC] Combining arrays arrays from different tissues and different labs.

[marco zucchelli]

Hi,

I would like to  check for differential expression on arrays
downloaded from public databases.
I was reading somewhere that it might be not very wise to normalize
together arrays produced from different tissues and different labs.

In practice I would like to compare mouse embryos from one experiment
with mouse adult tissues from another experiment.

Does somebody have an opinion on this ?

I tried to normalized the adult arrays and the embryo arrays
separately, rescale them to the same median and then extract the
expression values from all the arrays together (with li.wong method).
I tried also to normalize and extract the expression values for all
the arrays together with the same method. The results seem to be
pretty similar.

In this case the amplification protocols used are different since
embryo material is very small..

Best regards


Marco