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yezhengSTAT / ADTnorm

ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.
https://yezhengstat.github.io/ADTnorm/articles/ADTnorm-tutorial.html
GNU General Public License v3.0
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Error in chol.default(temp): the leading minor of order 11 is not positive definite #11

Open MartaCasado opened 1 year ago

MartaCasado commented 1 year ago

Hello!!

Thank you for this tool! I am currently trying to run ADTnorm in a dataset with 45 antibodies and 97K cells. I am using the following code: 

cell_x_feature$sample = factor(unlist(cell_x_feature$sample))
cell_x_feature$batch = factor(unlist(cell_x_feature$sample))

cell_x_adt_norm = ADTnorm(
  cell_x_adt = cell_x_adt, 
  cell_x_feature = cell_x_feature, 
  study_name = study_name,
  marker_to_process = NULL,
  bimodal_marker = NULL)

It seems to run smoothly until reaching the normalization of a specific antibody, when I get this error:

........Error in chol.default(temp) : 
  the leading minor of order 11 is not positive definite
In addition: There were 40 warnings (use warnings() to see them)

Do you know what could be causing it? Thank you! Marta

yezhengSTAT commented 1 year ago

Hello Marta, The error message does not look familiar to me.......maybe try generating the raw density plot using the arcsine transformation? See anything unique for this antibody. Or maybe just skip this one for now. I am working on the updated version. Hopefully the error message can be gone then.

Thanks, Ye