I am trying to use pathview to map my transcriptomic data. I don't want to perform pathway analysis, only get an overview how the expressed genes are related and take advantage of the nice visualization of up and down regulation by the different treatments.
I am working on a non-model species, so not present in the Kegg database. That might be part of the problem but very few genes map on the pathways... If I use kegg mapper for example, I get many more hits...
Moreover, I got a result that I can't make sense of: I used a subset of my data, for simplicity sake, at first. then, I used the whole data (so this previous subset plus more data) and the output pathways were different... both times I mapped to the same species and set the pathway to "auto". Does anyone encounter similar problems?
I wonder if this has something to do with "gene id type" used. I had more successful results using "Entrez" but it is not available anywhere how exactly is the format they require for each gene id type.
I get errors like this even though I chose the species from the drop-down list and I am certain of the id used.
- error in kegg.species.code(species, na.rm = t, code.only = f) :
Wrong species, gene or pathway ID specified, Or the uploaded gene/compound data is not in the requested format