I am currently working on an RNA-seq meta-analysis project. The first part of the project requires me to download three RNA-seq datasets, identify DEGs and perform meta-analysis using the robust rank aggregation method explained here by ATpoint .
The next part of the project requires me to validate my findings on two separate RNA-seq datasets. This is the part where I am facing an issue. The list of ranked DEGs obtained by the "RobustRankAggre" method produced 816 genes in total. However, out of these 816 genes, only 768 and 801 genes are present in the two validation datasets. This is preventing me from validating the model. I suspect that this might be an issue because of the sequencing platform variation between the derivation and validation datasets. If so, can anyone suggest a better method to combine DEGs obtained from multiple datasets and validating them eventually? TIA.
