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.
How to get fold changes from MetaDE package in R?
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.
• 2,649 views
•
link
updated
by
ATpoint
•
written
by
humbertojirey •
•
written
by
humbertojirey •
1 answer
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.
• 0 views
•
link
written
by
humbertojirey •
Log in to answer this question.
More posts like this
-
To identify Differentially Expressed Genes and Unraveling Upregulated and Downregulated Genes using…
written by Nelo •
-
Fold change cutoff for downregulated genes
written by blz •
-
Calculation of Fold change for already log transformed gene expression data
written by Bioinformatic •
-
Interpretation of results from ssizeRNA power analysis
written by anamaria
-
How to run a meta-analysis of differentially-expressed genes
written by monkey-bars •
-
how to calculate the log FC for -1.5 fold change?
written by Calangoa •
-
Imbalance up and down regulated genes
written by Angela •
-
Subsampling procedure for differential analysis
written by Vasu
-
range of fold change in RNA seq
written by kanwarjag
-
Statistical test to compare the number of upregulated genes in a subgroup of genes versus all genes?
written by biostart
If I may ask, why are you using a package that's no longer being maintained nor on
CRAN?Do you know another package that find DEGs with differents studies? And I can get the fold changes? Thanks for respond.
I don't quite understand what you mean by "DEGs with differents studies".
I mean finding differential expression genes with different studies or different GSE from GEO.
Have you looked through this paper?
This is the full list of
Rpackages they mention:MetaOmics,MetaIntegrator,MetaP,GeneMeta,metaMA,metaRNASeq,RankProd,RankAggreg,OrderedList,metahdep,metaSeq,MetaVolcanoR, andcrossmeta.They also mention a couple of web applications that can perform meta differential expression analysis.