SaskiaFreytag
commented
1 year ago Hi,
Labelling is never quite as easy as simply taking the most predicted annotation label in a cluster for the true label. Additionally to looking at this, we also looked at gene scores of known marker genes to make our final determination. I know that this might not be super satisfying but I don’t think labelling is a straightforward problem.
Cheers,
Saskia
From: Koh @.> Date: Monday, 27 March 2023 at 12:50 am To: ListerLab/pfc_development @.> Cc: Subscribed @.***> Subject: [ListerLab/pfc_development] scATAC-seq cluster annotation (Issue #9)
Hi, Chuck
I have a question about the process of annotating clusters in the scATAC-seq data. When annotating the scATAC-seq clusters, you integrated it with the scRNA-seq and calculated the confusion matrix of the "predicatedGroup". And then you confirmed that the cluster with the highest value was added as the "Cluster_sub". However, you didn't label it right away and added an annotation using a separate table scatac_clustering_annotation.xlsx. Can you tell me why you proceeded like that? In ArchR,
Thanks,
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koh2ng0
Hi, Chuck
I have a question about the process of annotating clusters in the scATAC-seq data. When annotating the scATAC-seq clusters, you integrated it with the scRNA-seq and calculated the confusion matrix of the "predicatedGroup". And then you confirmed that the cluster with the highest value was added as the "Cluster_sub". However, you didn't label it right away and added an annotation using a separate table
scatac_clustering_annotation.xlsx. Can you tell me why you proceeded like that? In ArchR,Thanks,