Comments (4)
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Thanks Sofie, that's very helpful! Just a follow up clarification regarding the plot: you mentioned that underneath the CV values you get "the different metacluster percentages for each of the files", is that the percentage of cells in each metacluster per batch?
Best,
Emma
from cytonorm.
Hello @SofieVG @jacobpwagner ,I am getting an error "Error in t.default(data) : argument is not a matrix "when I use testCV function.
How do I resolve it?
Thank you
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@emmanuelaaaaa
Hi Emma, apologies for the delay in reply but this is indeed what I meant. So percentages over all metaclusters will add up to 100% for each batch. This can help to estimate whether a potentially large CV is due to the fact that a cluster is a very small or whether it is still a change you would find problematic.
@Rashmi-pixel I think this might be due to you having an updated version of the FlowSOM package but not the latest version of the CytoNorm package. Please ensure you have the latest version installed. If the problem still occurs, feel free to open a new issue.
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Related Issues (20)
- Update needed for FlowSOM object update? HOT 3
- script is interrupted and doesn't produce output
- combine cytonorm with PeacoQC? HOT 2
- Cytonorm creating highly negative or very large values HOT 6
- testCV() Error in t.default(data) : argument is not a matrix HOT 4
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- Error in t.default(data) : argument is not a matrix
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- Normalization question HOT 2
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- CytoNorm for anaconda install HOT 3
- Error in the step of training the model HOT 2
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- Reading fcs files generated through PeacoQC by Cytonorm
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