How to set median data in transcriptomics explorer in mouse datasets? currently, only trimmed means data are seen in the heatmap
Hi Christos,
Both trimmed means and medians are available for download for each dataset, but currently only one option is available for visualization in the Transcriptomics Explorer.
Do you generally prefer medians, or would you want the option to toggle / compare the two?
Hello,
thank you for the response. I would prefer to have the option of toggle the two.
In order to view the dataset, a supercomputer is needed, I cannot filter out for the genes that I am interested and do a heatmap plot in R or Origin with a relatively good workstation PC.
Best regards,
Christos
I agree that this is a huge dataset and very demanding of compute resources!
That said, we’ve tried to set up the Transcriptomics Explorer to support common forms of investigation. For example, you can add one or many genes to the heatmap, and you can visualize the expression for a single gene across the entire dataset in the Scatterplot view.
When you say “filter for the genes I am interested in,” what kind of operation are you trying to achieve?
Hello Tyler,
I am interested in comparing the neuron vs non-neuron mitochondrial protein expression in mice vs humans. I could use the tool by adding 50 genes at a time (out of 1000 from MITOCARTA), but I can only compare mouse median data with human trimmed mean data. Thus, I cannot really compare the mouse vs the human.
Best,
Christos