Hi,
If this is not the right website where to ask this question please re-direct me where it is more appropriate. That's more an "interpretation results" question rather than a problem with a script.
Today notice that Reactome website has a new analysis tool function called "gene expression analysis" that allows comparing multiple datasets by just importing your gene list/dataset so I did try just to see what was the output of the analysis in case it was useful tool to use for future analysis. So I did upload 3 dataset as they clearly show in the website but I am a bit confused on the interpretation of the results and I could not find any tutorial page for that (I wrote an email to the help support but since they haven't replied yet I was thinking to ask this community for more clarification).
Looking at the PDF report I obtain as output: I: number of pathway identified in each dataset
II: an heatmap with the enriched term per dataset showing if the pathways are shared between dataset and if the genes identified are up or down regulated
am I right?
III: the expression of genes associated with pathway X and the barplot of the gene expression of the samples? Like in the image attached the top 1 term for dataset 1 is “mitochondrial biogenesis” and then I see the pathway expression of all the samples of all my dataset to see whether those genes identified in that specific term are either up or down regulated?
Is any of my assumption correct?
Thank you for the help and apologies if the post is not appropriate for this community (I did not known where it was best to post it)
Camilla
Your images are broken, and you might find this helpful https://bioconductor.org/packages/devel/bioc/vignettes/ReactomeGSA/inst/doc/using-reactomegsa.html