No Instructions for Tissues and Cell Culture Merging

immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

https://portals.broadinstitute.org/harmony/

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No Instructions for Tissues and Cell Culture Merging #240

Closed DarioS closed 8 months ago

DarioS commented 9 months ago

Would be nice to have advice in the user guide for merging cancer tissue and patient-derived cell-culture. They aren't merging.

pati-ni commented 9 months ago

Please provide a few more details. Does the code throw an error, or harmonized populations are not adequate?

On Fri, Feb 2, 2024, 18:00 Dario Strbenac @.***> wrote:

Would be nice to have advice in the user guide for merging cancer tissue and patient-derived cell-culture. They aren't merging.

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DarioS commented 8 months ago

The harmonised populations stay separated. There is no error message.

pati-ni commented 8 months ago

Should the tumor cells merge?

What about the rest of cell types, are these separated?

Can you share the objective function plot?

Have you tried higher values of theta?

On Thu, Feb 15, 2024, 04:00 Dario Strbenac @.***> wrote:

The harmonised populations stay separated. There is no error message.

— Reply to this email directly, view it on GitHub https://github.com/immunogenomics/harmony/issues/240#issuecomment-1945641505, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSFW2H54VBDHQ6BYPJBCOTYTXFB5AVCNFSM6AAAAABCXNJDCSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVGY2DCNJQGU . You are receiving this because you commented.Message ID: @.***>

DarioS commented 8 months ago

I am unsure if cancer cells from tissue and cell culture should merge. That is a tough biological question. I have not seen anyone else with the same kind of paired data. Is there such a data set within Broad Institute which you could try? I can't share the one which I am working on. Cell culuture contains only two cell types; cancer and cancer-associated fibroblast. Tissue contains eight cell types. Wouldn't lower values of theta be recommended? I want the data to merge more, not less. I tried 0.

pati-ni commented 8 months ago

Can you share UMAPs before and after the integration of the two datasets? Also, theta needs to be increased to force the cells together. Setting it to zero disables the low batch diversity penalty.

DarioS commented 8 months ago

Ah, O.K. increasing theta is the solution which leads to good mixing.