meta-analysis to multiple RNA-seq differential studies

Question

[Shicheng Guo]

Dear All,

I want to perform a meta-analysis to several gene expression differential analysis studies with R. What I have includes log2(FoldChange), raw P-value, differential expression test (GLM and Chi-square) and total sample size. Anyone can share the strategy how to make this meta-analysis reliable?

Thanks. Attached is an example data:

https://github.com/CNAID/mRNA/blob/master/meta.csv

Answer 1

[ATpoint]

Without being an expert on the matter I found the arguments for a rank-based meta-analysis quite convincing, see the paper https://academic.oup.com/bioinformatics/article/28/4/573/213339 and the associated R package https://cran.r-project.org/web/packages/RobustRankAggreg/RobustRankAggreg.pdf

I tried to summarize my understanding why rank-based meta-analysis makes sense here in this answer: A: remove Batch Effect between several **RNA-seq** studies (no replication) Again this is my naive (not-being-a-statistician) opinion.