A complete tutorial on how to use GEO2R to perform differential expression analysis on any of the available GEO gene expression datasets is available here. After selecting the studies and running GEO2R. The results have to be exported and then upload to Metavolcano. Make sure your exported results contains the "ID", "adj.P.Val", "P.Value", "t", "B", "logFC", "Gene.symbol" and "Gene.title" columns.
Each GEO2R result file should look like this:
The user first has to set a significance and a log2 fold-change threshold to define the differential expressed genes by study. For significance, the user has to set first either "adj.P.Val" or "P.Value". Once both parameter were settled, Metavolcano will display the result per study and a cumulative frequency of genes being consistently perturbed. Based on the user-desired number of consistently perturbed genes, the user can then settle the consistency threshold parameter which range among 0 and 1.
"adj.P.Val" or "P.Value"
A number among 0 and 1.
A number among 0 and Inf.
A number among 0 and 1 indicating the proportion of studies where the gene has to be consistently perturbed to be consider as consistently and differentially expressed.