I would like to do meta-analysis on the public data of RNA_seq downloaded from several studies. which packages do you recommend for differential expression? Can I use meta DE that is specific for microarray? I have already downloaded the data and have done quality control by CLC. Thanks in advance
If all your datasets were sequencing by RNA-seq you can use some R package like DEseq2 or Edje2 but you have to take care about how this rna-seq was performing (Bulk RNA, PolyA-RNA, rRNA deplection) and the technology that was used (Ion torrent, Illumina, etc). Depending of this, probably the pre-procesing of the datesets won't be the same.