Question: Analysis of ratios (fold changes) from different microarray experiments with common control
gravatar for matt.arno
4.5 years ago by
United Kingdom
matt.arno0 wrote:

Hi - I have two gene expression experiments that I performed on microarrays at different times:

expt 1: 3x untreated controls 3x treatment A

expt 2: 3x untreated controls 3x treatment B

note: the untreated controls are from the same RNA in both experiments.

Whilst I can easily determine treatment A and B effects separately, I would also like to find out what is statistically different between A and B. I can do a Venn diagram to see what is unique and common to both lists, but I was wondering whether there was a more statistical method.

I thought that perhaps I could normalise the treatment signals to the relative average control signal in each case, and then compare these ratios (A/CTRL vs B/CTRL) to each other in a t-test or similar.

Or make a joint experiment with all 12 samples and somehow construct a linear model to take into account the control groups measured twice.

Thanks for any help

Cheers, matt

ADD COMMENTlink written 4.5 years ago by matt.arno0

I guess you could get an idea of (severity of) potential batch effects by doing the comparison of the control samples in both runs against each other.

ADD REPLYlink written 4.5 years ago by WouterDeCoster45k
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