In the summary methylation plot, we discussed, EpiExplorer takes into consideration only the methylation ratio. Keep in mind that this plot is only intended to provide intuition about the data.
In case, you want to inspect after you apply additional filters, I suggest you filter out your regions for number of CpGs (and/or coverage) and then you can inspect the details of the distribution of methylation ratios.
You can see an example here: http://www.slideshare.net/khalachev/step-by-step-guide-to-figure-1
The methylation chart reports what percent of the regions in your datasets that can be considered methylated or unmethylated based on their methylation ratio for a specific tissue. The methylation ratio of each region (e.g. exon, gene, promoter, CpG island) is computed by averaging the methylation for every CpG for which there is methylation data available for the tissue. If the ratio is below 0.33 the region is considered unmethylated and if it is above 0.66 it is considered methylated.
Hope this helps,
Can you please specify the data for which chart do you want to have available?
Every chart has a 'to table' button where the numbers from the chart are shown and exportable.
Also every chart has a 'to png' button so that you don't need to use printscreen
You can export the control regions.
The control regions are an EpiExplorer dataset of its own. This means that you can interact with it and export the full dataset or any subset the same way as any other EpiExplorer dataset. You can read moreif you open the "Saving, exporting and sharing EpiExplorer results" slideshow from the starting page of EpiExplorer, more specifically slide 6.
Should be working now. Please try again
I'll look into it immediately. I'll respond here as soon as we fix this
If you are planning a larger rat project we would certainly consider contributing. If this is the case, please contact our corresponding authors with more details (http://genomebiology.com/2012/13/10/R96). Otherwise, in order to be worth setting things up, we would need serious user interest in this genome that we have not yet observed.
You can visit http://epiexplorer.mpi-inf.mpg.de
If this does not answer the question, can you please give more details on what do you mean?
Thank you for noticing and notifying us. It should be working fine now.
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