Hi,

I have Tumour and Normal technical replicates run on both FFPE and
RNA-Later.
These are run on X3P arrays. I am interested in comparing the outcome from
both
fixation methods. When I compare the transcripts classed
as expressed in both RNA-Later and FFPE the ones found
unique to FFPE is very small (<5%) - if I assume the RNA-Later
samples exhibit true expression levels this is a good result.
The intensities/background from both fixation methods is almost
equal as well.

When I look for differential expression between tumour/normal using
both fixation methods. I find that almost half of what is differentially
expressed in FFPE is not differentially expressed in RNA-Later. This
disagreement would indicate that the differential expression in FFPE
is peppered with false-positves or that RNA-Later is not picking up
differential expression - I'd guess it is the former.

The tests for differential expression was done using CyberT, SAMR and
Muilttest,
and a modified t-test. Does any one have any ideas what other testing
methods would
be worth investigating, or have any idea why there is so many false
positives
in FFPE?


Thanks,

Martin

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