gold standard mRNA differential expression

Question

[Jan-Niklas]

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

Answer 1

[michael.ante]

Hi Jan-Niklas,

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

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

[Jan-Niklas]

Thanks a lot, Michael. Pointed me in the right direction. However, I came across these two studies, which seem perfect for my purpose. Wanted to share them with everbody interested:

Breast cancer data set Golden Spike data set