I have a conceptional question,I have several RNA-seq experimentS (tretment /control),I did meta-analysis with expression value,on the other hand I did differential expression ( all treated vs all controls) with DEseq2. for 2 of them I should filter and select effective genes,now I want to know what is the difference between meta analysis and differential expression( all treated vs all controls) ?
Meta analysis of expression is commonly if you have multiple experiments in which you perform differential expression analysis, and combine those results. Within one experiment you just do differential expression analysis comparing treatment vs controls.
Say that you did your experiment on 5 treatment samples and 5 control samples and want to compare your results with the results of a friend who used another technology with 8 treatment samples and 4 control samples, then you both have done a differential expression analysis on your own data, and combining the data for a joint analysis would be a meta analysis.