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navinlabcode / copykat

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confusion of prediction results #56

Closed songmingl closed 1 year ago

songmingl commented 2 years ago

Hello, I'm using copykat (version 1.0.8), and everything go well, but found that there were multiple predicted results for one cell barcode, for example:

image

the cell TTTGTCAGTCATATCG-1 was predicted as aneuploid and not.defined, I'm confused about this, why did this happen, and any suggestions for results like this?

q541425866 commented 2 years ago

I got the same problem. Have you solved it？

songmingl commented 2 years ago

I got the same problem. Have you solved it？

No, but I test some samples, and it seems that only not.defined results would be duplicated, I haven't seen any cell predicted as aneuploid and diploid at the same time. So, I just removed all not.defined records.

I also noticed in the tutorial, step 4: This version put back all filtered cells and label them as "not defined" cells. If the not.defined cells were filtered, it's still confusing why filtered cells will be predicted as aneuploid

q541425866 commented 2 years ago

I got the same problem. Have you solved it？

No, but I test some samples, and it seems that only not.defined results would be duplicated, I haven't seen any cell predicted as aneuploid and diploid at the same time. So, I just removed all not.defined records.

I also noticed in the tutorial, step 4: This version put back all filtered cells and label them as "not defined" cells. If the not.defined cells were filtered, it's still confusing why filtered cells will be predicted as aneuploid

OK, thank you.

xjin15 commented 2 years ago

I have the same confusion, and i also found another issues, Hope the author give an explanation. #31

gaobio commented 1 year ago

thank you for reporting this issue. @songmingl @xjin15 @q541425866 @Puriney. It was caused by an error in indexing cells. I forgot to change it back to general index after testing the example data set. It should be addressed now. In your previous results seeing both 'aneuploidy or diploid' prediction and the 'not.defined' results, you could use the formal as the true results.

zhouyao315 commented 1 year ago

Hello, I'm using copykat (version v1.1.0), and found that there were multiple problems, for example: 'WARNING! NOT CONVERGENT",Will it affect my results? and what cause this? @gaobio