affymetrix vs cDNA microarray conflicting results help - (Jun/01/2006 )

Hi!

I'm new in analysing microarray data and need some insights! Please!
I'm looking at 5 different studies (3 affymetrix, 2cDNA) on breast tumours. I looked at the expression of a specific gene and looked at whether patients which tumours express low level of this gene do better (in disease-free recurrence) compared to tumours with high level of expression.

However, affymetrix results contradict cDNA (2-colors) microarrays, both with a significant p value. Which one should I trust.

Thanks!

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Hi.

I suppose ANY expression studies using microarray need to be confirmed by independent methods, and real time PCR is the most often used now. Do not rely on "p". There are too much causes to get hybridization difference besides expression level, the most important are "hybridization ability" (inner hairpins etc), kinetics and parasite homologies of each individual probe.

Short probes may have a lot of homologies in many genes. The longer Your probe the more specific it may be but chances to get a parasite homology from other genes grow again.

And, of course, all these studies may give contradict results because of different properties of tumors the authors used - You should know that each individual tumor has a lot of differences even from tumors of the same tissue origin.

So, You may first take sequences of oligo/cDNA that differs in the studies You have read and Blast them. If they all good and specific, try to compare clinic properties of the tumors, it may be also that all results are true.

But, again, confirmation is needed for each gene by independent method.

I'd like to glance at these articles...

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