Hi there. I have been exploring how Augur is filtering out genes and therefore looking more closely at the select_variance function. The reason I wound up on this track is because one of the cell types I was expecting to be rankly highly by Augur (based on previous DE gene analysis) was not performing well, and when I dug into the output of Augur, it looked like the most significant DE genes from previous analysis were getting filtered out using the default var_quantile 0.5 threshold. So I've been trying to understand why.
Upon looking more closely at the select_variance() function, it looks like in the comments you intend to calculate CV (sds / mean), but in the actual code, you are calculating a form of Z-score (mean / sds). If this is what you are meaning to calculate, can you explain a little more conceptually how this is filtering out the genes with the lowest variance? Using (sds / mean) makes more sense to me, but perhaps I am misunderstanding the goal of this step.
Thank you for maintaining this tool and thank you for your help!
Hi there. I have been exploring how Augur is filtering out genes and therefore looking more closely at the select_variance function. The reason I wound up on this track is because one of the cell types I was expecting to be rankly highly by Augur (based on previous DE gene analysis) was not performing well, and when I dug into the output of Augur, it looked like the most significant DE genes from previous analysis were getting filtered out using the default var_quantile 0.5 threshold. So I've been trying to understand why.
Upon looking more closely at the select_variance() function, it looks like in the comments you intend to calculate CV (sds / mean), but in the actual code, you are calculating a form of Z-score (mean / sds). If this is what you are meaning to calculate, can you explain a little more conceptually how this is filtering out the genes with the lowest variance? Using (sds / mean) makes more sense to me, but perhaps I am misunderstanding the goal of this step.
Thank you for maintaining this tool and thank you for your help!