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I noticed some inconsistencies between the results produced by Seurat 5 and previous versions. In the integration process of Seurat 5, it seems that there is no creation of a new 'integrated' assay as in previous versions. The official explanation mentions, 'The Seurat v5 integration procedure aims to return a single dimensional reduction that captures the shared sources of variance across multiple layers, so that cells in a similar biological state will cluster.' Does this mean that in the new process, the integration process does not adjust the data itself? I also compared the data before and after integration, and it seems that the data in 'scale.data' does not change before and after integration.
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I noticed some inconsistencies between the results produced by Seurat 5 and previous versions. In the integration process of Seurat 5, it seems that there is no creation of a new 'integrated' assay as in previous versions. The official explanation mentions, 'The Seurat v5 integration procedure aims to return a single dimensional reduction that captures the shared sources of variance across multiple layers, so that cells in a similar biological state will cluster.' Does this mean that in the new process, the integration process does not adjust the data itself? I also compared the data before and after integration, and it seems that the data in 'scale.data' does not change before and after integration.
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