Can I identify differential expressing genes of 2 samples using only 4 chips?

Question

[Avis]

I would like to identify differential expressing genes of 2 samples, however, I only have 4 chips, 2 chips for one sample ( Gene 2.0 ST Array, Affymetrix). Is it possible to identify statistical significant expressing genes? I have Partek on hand for analysis. Thank you

[Irsan]

yes, that is possible. It is also very well possible that the power of your analysis is low. It also seems like you have 2 technical replicates per condition, which is a waste of money. If you have only one biological replicate, it is still possible to see what genes are differentially expressed between your two conditions, although this will not tell much about other biological samples ... (N=1)

Answer 1

[Benn]

Ask your Partek support team for help! I never work with commercial tools, and most people here use open source tools for their analysis. If you pay for a tool, I expect that it will include support from them as well?

[russhh]

I don't think commercial support can be held responsible for experimental design - that should be the bread and butter of a research scientist (I personally wouldn't waste my time with a 2x2 experiment)