Although this topic has been discussed in the past in several other occasions, i am curious to know your current opinion about that. Several methods have been proposed and i would know from you how you would deal with combining several microarray and RNA-seq experiments for whatever purpose (DE-analyses, Gene Regulatory Networks, etc..), thus how would you address problems as removing batch effects and transform/normalize the data before processing it.

If you can please cite some relevant paper on that.

Thanks in advance

( 1. Combining Gene Expression Microarray Datasets 2. workflow for combining multiple microarray studies of same platform 3. https://www.researchgate.net/post/How_can_you_combine_different_published_expression_datasets_and_analyze_them_in_R 4. Combining Microarray and RNAseq data 5. methods of integrating microarray data and RNAseq data 6. Is it possible to combine micro array data and RNA-Seq data and perform meta analysis for differential gene expression analysis. 7. Combined Rnaseq + Microarray Transcriptomics Datasets 8. Integrating Different Data Types To Infer Gene Regulatory Networks 9. https://support.bioconductor.org/p/75246/ )