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

zhaodj zhaodj at ioz.ac.cn
Tue Sep 22 16:46:54 CEST 2009

 Have you ever checked the original microarray images? Sometimes some 
badly-printed spots may pass the QC and lead to this kind of weired 
problems. Chances are higher if you have less replicates. I'm just 

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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