[BioC] Different expression direction between limma microarray data analysis vs quantitative real time PCR result

Francois Pepin fpepin at cs.mcgill.ca
Mon Sep 21 16:31:36 CEST 2009

Hi Wang,

Is it 2 genes out of say 10 (or more), or two genes out of two?

If it's two out of 10 and the others worked out properly, I would go 
with Naomi and say it's probably just a false discovery.

If you only checked two, the first thing that comes to mind is that you 
had the samples switched at some point, either on the microarray side or 
the PCR side. In this case, you might want to do a few more genes to see 
what's happening.


jixinwang at tamu.edu wrote:
> Dear all,
> I use limma package to do microarray data analysis and most of real time PCR validation results are consistent with microarray data in terms of expression direction and statistical significance. However in one set of experiemnts, two DE genes are statistically significant in both of microarray and qRT-PCR result BUT had the different expression direction. (e.g. They are  down regulated in microarray result but real time PCR result showed that they are up regulated)? I don’t know why. Does this occur to anyone before? Many thanks.  
> Best regards,
> Wang
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