Hi @mshtrahman ,
As you’ve noted, in all heatmaps, the downloaded values match exactly what is shown on the screen. As for why the values don’t match, they should, so I’m not sure. Unfortunately the data for this project was done a long time ago from by a collaborator group so I don’t know if we’ll be able to track down an answer, but I’ll try and will post an update if I learn more.
One possibility is that the heatmap is still showing the Gencode v3c data rather than the newer Gencode v10 data (which could be checked). Another is that the heatmap is using a slightly different normalization, but that seems unlikely.
As for the N/A vs. 0 question, N/A means 0. This only shows up in genes with low expression and all samples have data collected for the exact same set of genes.
This post might provide some additional context.
Best,
Jeremy