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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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Error in NORMAL_COUNTS_tot #167

Closed bwubb closed 7 months ago

bwubb commented 7 months ago

Greetings,

I am receiveing the following error during prepareTargetedSeq

...
Done reading locis
Multi pos start:
Reading locis
Done reading locis
Multi pos start:
Error in NORMAL_COUNTS_tot[INDEX_nonPAR, INDEX_XX] :
  subscript out of bounds
Calls: ascat.prepareTargetedSeq ... getLociFromNormals -> which -> rowSums -> is.data.frame
Execution halted

I believe there are 4 or 5 normal samples that are removed for low coverage or low snps. Could that be the cause? I was able to successfully run ASCAT in a smaller 3 tumor/normal pair selection, but when I extend the analysis to the full set (147 pairs), I can not get through this step.

Thank you

-bwubb

zhangzhhcb commented 7 months ago

I may need more details to answer your question, like what mode of ASCAT are your using? About the sample you removed, did you remove matched tumors as well? Have you tried as your add those samples back?

bwubb commented 7 months ago

Removing the normals and their tumor pairs did get passed the error. In hindsight this should have been the obvious thing to test, my apologizes. Thank you for the replay.