How to get fold changes from MetaDE package in R?

Question

[humbertojirey]

I am using MetaDE to find differential expression genes in different studies. All articles says that the way to find upregulated and downregulated genes is with the fold changes (FC), but results from MetaDE dosent show FC, just a stat (that i dont now what it means) and the pvalues and FDR. Is the stat the fold changes? Or is the stat from the individual analysis from each study.

[Dunois]

If I may ask, why are you using a package that's no longer being maintained nor on CRAN?

[humbertojirey]

Do you know another package that find DEGs with differents studies? And I can get the fold changes? Thanks for respond.

[Dunois]

I don't quite understand what you mean by "DEGs with differents studies".

[humbertojirey]

I mean finding differential expression genes with different studies or different GSE from GEO.

[Dunois]

Have you looked through this paper?

This is the full list of R packages they mention: MetaOmics, MetaIntegrator, MetaP, GeneMeta, metaMA, metaRNASeq, RankProd, RankAggreg, OrderedList, metahdep, metaSeq, MetaVolcanoR, and crossmeta.

They also mention a couple of web applications that can perform meta differential expression analysis.

Answer 1

[humbertojirey]

Thanks for the answers, if fold changes is not used in meta analisis how can I know if a gene is upregulated or downregulated with the moderated t statistic resulting from individual analisis.

[ATpoint]

Each individual analysis returns typically a fold change and some kind of stat (e.g. a pvalue). This tells you whether a gene is over-or underexpressed. The meta-analysis then aims to tell whether this pattern of expression change is consistent between multiple datasets.