Comments (7)
Hi again, Could you clarify this for me please?
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Thanks for the comment, It was indeed very useful.
I'm still not sure for the case of lymphomas how can I make the reference. the samples are very variable regarding their composition of immune cells. Have you ever bench marked your method agains using different ref expressions?
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Yes, we are currently dealing with the same types of challenges; I have some leukemia datasets that comprise many immune cell types. My solution has been to identify cell types first using dimensionality reduction + clustering approaches such as pagoda2 (https://github.com/hms-dbmi/pagoda2), and then perform HoneyBADGER analysis for each cell type using the appropriate sorted immune cell reference from 10X. You will definitely need to check that any subclonal alteration you identify is not simply contamination from another cell type.
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Thanks, I'm calling cell types using Seurat and the call CNVs using Honeybadger. I was not able to find any CNVs, I'm not surprised with this though since the cancer I am working on is silent in terms of CNVs or the CNVs are very focal. Thanks again for taking the time to respond to the issues here. Good luck with the paper!
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Hi Jean--sorry to dig this up. Just wondering if you had any insight into how close the reference expression should be? Eg. For carcinomas that arise from epithelial cells that represent a small percentage of the bulk tissue they reside in, is the bulk tissue appropriate? Working on ovarian cancer and healthy epithelium makes up a small amount of the organ. I could try bulk RNA-Seq from cultured epithelial cells. Any thoughts about this?
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Related Issues (20)
- lt$setGexpDev HOT 1
- Warning in setGeneFactors and error in retestIdentifiedCnvs
- Allele-mode for selecting normal cells HOT 2
- 10X + Honeybadger question HOT 2
- Error in summarizeResults HOT 3
- Error in calcGexpCnvBoundaries when running with numeric chromosome names HOT 1
- Error: subscript contains invalid names HOT 9
- read bam files HOT 4
- Filtering of identified CNVs HOT 2
- speed of running setAlleleMats step
- What is the reason for only including snps in HoneyBADGER? HOT 2
- gene filtering different in HoneyBADGER object HOT 3
- Error: Failed to install 'HoneyBADGER' from GitHub HOT 2
- Showing error when trying Getting_Started.Rmd
- no method for coercing this S4 class to a vector HOT 3
- showing NULL in the step of calcGexpCnvBoundaries - getting started tutorial HOT 12
- Applying bayesian hierarchical model in integrating analyses tutorial
- error in hb$summarizeResults
- Error in summarizeResults for the allele-based approach
- Error in calcCombCnvProb HOT 1
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