Errors in MarkerBasedDecomposition about bisque

[brandonjew]

Hi Frank,

We diagnosed the bug and will push the fixes soon. The errors are due to a cell-type with only one marker gene. This should be avoided since the marker-based decomposition uses a PCA-based approach that does not apply to cases with only one gene. I'll let you know when the package is updated.

Thanks,
Brandon

[brandonjew]

Package has been updated on GitHub. Let me know if there are still any issues. The update has not propagated to CRAN or Bioconda yet, so you'll need to manually update if you need it immediately

[yuewangpanda]

Thank you for the updates. It works well now. Still have a quick question: what are the values of the bulk.props? My understanding is the weight of the similarity of a sample (bulk) and a cluster (single-cell). Correct me if I don't get it. Thanks, Frank

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On Fri, Dec 6, 2019 at 8:15 PM Brandon Jew ***@***.***> wrote: Package has been updated on GitHub. Let me know if there are still any issues. The update has not propagated to CRAN or Bioconda yet, so you'll need to manually update if you need it immediately — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#7?email_source=notifications&email_token=AI2CASBG3PMMJT5253D34NLQXL2KHA5CNFSM4JU6HG62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGFZ7IY#issuecomment-562798499>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI2CASE5UB34VZTPLHWXDNLQXL2KHANCNFSM4JU6HG6Q> .

[marcalva]

Hi Frank, the bulk.props contains (relative) cell type proportions estimates for each sample. These are principal component scores and so they do not represent true proportions. So samples with higher values for a cell type will have overall higher expression of that cell type's marker genes. Hope this make sense!

Thanks,
Marcus

[yuewangpanda]

Hi Marcus, Clear explanation. However, in my case, some of the values are negative. Is it correct? Best, Frank

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On Mon, Dec 16, 2019 at 3:17 PM marcalva ***@***.***> wrote: Hi Frank, the bulk.props contains (relative) cell type proportions estimates for each sample. These are principal component scores and so they do not represent true proportions. So samples with higher values for a cell type will have overall higher expression of that cell type's marker genes. Hope this make sense! Thanks, Marcus — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#7?email_source=notifications&email_token=AI2CASHVG6MHSNIITAF3O6DQY7O65A5CNFSM4JU6HG62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEG76TSQ#issuecomment-566225354>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI2CASCHMBP2JKVN47DMEGLQY7O65ANCNFSM4JU6HG6Q> .

[marcalva]

Hi Frank,

That is correct. Some values can certainly be negative.

Best,
Marcus