Dear all,

I am working on a method which combines the results of two procedures (limma, GSEA) to identify differentially expressed genes/pathways to obtain even better results using a simple machine learning approach.
For this, I need some kind of gold standard to compare my results with. So my question is: Does somebody know a dataset for which the results (up or down regulated genes/pathways) are known/sufficiently proved (e.g data set used by a paper)?
The data should be publicly available and microarray based.

Best regards,
Jan-Niklas

Hi Jan-Niklas,

please have a look at the SEQC experiments ([see here][1]) and the ABRF study (see publication [here][2]).

Both studies are based on the FDA-samples (A,B,C, & D) which are standardised mRNA-samples and have also been used in the MAQC studies for Microarray platforms. Both studies are publicly available at GEO.

Cheers,

Michael


  [1]: http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/#MAQC-IIIalsoknownasSEQC
  [2]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167418/