Moderator: igor
igor ♦ 11k
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Posts by igor
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... > TPM normalization (like any naive per-million scaling) is unable to
> properly correct for differences in library composition.
Yes, but it's not clear if any method can properly deal with sparse single-cell data. I keep hoping for someone to present an analysis where they demonstrate a diff ...
written 15 days ago by
igor ♦ 11k
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... I think you need `col.name` if you are adding a vector (so no obvious column name). If you are adding a data frame, there are columns with names already.
I would generally advise against `cbind` because you can't guarantee the same order. ...
written 17 days ago by
igor ♦ 11k
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... You can also just treat `seurat_obj@meta.data` as a standard data frame and modify it using generic functions. ...
written 18 days ago by
igor ♦ 11k
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... For the purpose of somatic/germline discussion, any germline/inherited SNV is a SNP and tumor-specific is somatic. For population genetics, you can have common and rare SNPs. They are germline either way. ...
written 20 days ago by
igor ♦ 11k
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... Germline SNVs are SNPs ...
written 21 days ago by
igor ♦ 11k
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... Yes. You also don't know the absolute copy number. For example, if the variant is at 25%, it could be 25% tumor (homozygous), 50% tumor (heterozygous), amplification of the non-mutated copy (1 mutant, 3 WT), some combination of those, or a more complex event. ...
written 21 days ago by
igor ♦ 11k
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... With germline, you know the original frequency is either 50% or 100%. With somatic, you do not. As you said, somatic variants are still informative. They can be used to estimate tumor purity and clonality, and there are specialized tools for that. ...
written 21 days ago by
igor ♦ 11k
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... I believe genetic data is considered PHI in the US ([source][1]). Of course, that would not matter if the participants give consent to release it.
[1]: https://www.hhs.gov/hipaa/for-professionals/special-topics/genetic-information/index.html ...
written 21 days ago by
igor ♦ 11k
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... > is there anything wrong with using somatic SNVs as well?
There will be a lot less of them, so the impact will be negligible. ...
written 21 days ago by
igor ♦ 11k
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Comment:
C: Negative values HTSeq2
... You may want to go through a basic R tutorial. If you plan on using DESeq2, you'll need to know some basics like what the different data types are and how to read/write files. ...
written 22 days ago by
igor ♦ 11k
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