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Doubt in sim_mean and ground truth #131

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cakeinspace opened this issue Dec 28, 2023 · 1 comment
Open

Doubt in sim_mean and ground truth #131

cakeinspace opened this issue Dec 28, 2023 · 1 comment

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@cakeinspace
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cakeinspace commented Dec 28, 2023

The muscat bioconductor page says that
Screenshot 2023-12-28 at 14 46 32
Where $\lambda_c$ is a cell dependent parameter. Now for each cell that we simulate the sim_mean for a gene should be different however when i look at the metadata(sim)$gene_info. It appears that each gene in each cluster and each sample has only one sim_mean values. Shouldn't it be different for each cell. Or is $\lambda_c$ chosen once for each cluster.

@cakeinspace
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After some digging around in the code base. What i think is happening is that the counts are simulated using $\mu_{gc}$ above. so each cell has its own $\mu_{gc}$. Then finally we average all the $\mu_{gc}$ for a cluster over the cells to report the $\mu_g$ for each gene in a cluster. Is this correct

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