I am looking for a public dataset that has RNA-Seq and Microarray samples from the same tissue &/ same conditions but I am interested in the RNA-Seq dataset that has batch effects. Can you please share the GEO id or Array Express link ?Thanks!
Researchers will not typically study batch effects directly if they have another end-point of interest, and may only make a loose reference to batch in supplementary methods. As such, it may be difficult to find the exact experimental set-up that you want.
However, you should be aware that the TCGA has expression data on various cancers as both RNA-seq and cDNA microarray, and, because it's the TCGA, most of these samples will overlap centers and therefore be from different batches. Take a look at the NCI's Genomic Data Commons to see what you can find.
Also take a look at these: