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Error with SCINA command #23

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Pedramto89 opened this issue Mar 17, 2023 · 16 comments
Open

Error with SCINA command #23

Pedramto89 opened this issue Mar 17, 2023 · 16 comments

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@Pedramto89
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Hello. When I run the following command, I get the eror:

Command:
results = SCINA(exp, signatures, max_iter = 100, convergence_n = 10, convergence_rate = 0.999, sensitivity_cutoff = 0.9, rm_overlap=F, allow_unknown=TRUE, log_file='SCINA.log')

Error:
Error in chol.default(theta[[i]]$sigma1) : 'a' must have dims > 0
@wtwt5237
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Hi @Pedramto89

Can you double check that indeed each cell type has at least one valid signature gene in the signatures object that you specified?

Thanks!

Tao

@Pedramto89
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Hi @wtwt5237
Thank you for your response. Yes there is.
image

@xiaocong3333
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I have the same problem, I even tried one different gene for one cluster, and the error still exists.
Error in chol.default(theta[[i]]$sigma1) : 'a' must have dims > 0
In addition: Warning message:
In min(c(diag(x$sigma1), diag(x$sigma2))) :
no non-missing arguments to min; returning Inf

@xiaocong3333
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image

@longyingda
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rm_overlap
A binary value, default 1 (TRUE), denotes that shared symbols between signature lists will be removed. If 0 (FALSE) then allows different cell types to share the same identifiers.

I also encountered this problem, but after I set this parameter to F, it can run normally, probably because there are some shared genes, and the marker of cell types with few genes changed to 0 after repetition, resulting in errors.

@longyingda
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image

rm_overlap
A binary value, default 1 (TRUE), denotes that shared symbols between signature lists will be removed. If 0 (FALSE) then allows different cell types to share the same identifiers.

I also encountered this problem, but after I set this parameter to F, it can run normally, probably because there are some shared genes, and the marker of cell types with few genes changed to 0 after repetition, resulting in errors.

But your problem should be that your some marker gene is not present in the expression matrix.

This was referenced Aug 3, 2023
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@LiMo-bioxer
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I also encountered the same problem, I wonder if it is related to the different gene names of humans and mice？

@longyingda
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I also encountered the same problem, I wonder if it is related to the different gene names of humans and mice？

  1. your signature lists contain many overlapped genes, set the parameter 'rm_overlap=FALSE';
  2. check that the name of your maker gene is correct, if the gene is present in your expression matrix;
  3. If a signature contains too many marker genes it will also report an error, 20 to 50 genes per signature is enough for good performance in SCINA.
    SCINA error message #8

@LiMo-bioxer
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I also encountered the same problem, I wonder if it is related to the different gene names of humans and mice？

  1. your signature lists contain many overlapped genes, set the parameter 'rm_overlap=FALSE';
  2. check that the name of your maker gene is correct, if the gene is present in your expression matrix;
  3. If a signature contains too many marker genes it will also report an error, 20 to 50 genes per signature is enough for good performance in SCINA.
    SCINA error message #8

I found that some of the marker genes were not in the expression data and could be removed for use. Thank you！

@martina811
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martina811 commented Jan 22, 2024 •
edited
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Hello everyone,
I noticed that a signature has to be at least 2 genes that are present also in the expression matrix, otherwise I got the same error message "Error in chol.default(theta[[i]]$sigma1) : 'a' must have dims > 0". Is it something that can be fixed from the code? So that if a signature does not have genes included in my expression matrix, this feature will not be taking into account.

Thank you all!

@mckoch234
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I am also running into this issue. I only used the example signature provided. Should I make a list for each celltype?

@wtwt5237
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wtwt5237 commented Jul 24, 2024 via email

@mckoch234
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mckoch234 commented Jul 24, 2024 via email

@wtwt5237
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wtwt5237 commented Jul 24, 2024 via email

@mckoch234
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mckoch234 commented Jul 25, 2024 via email

@mckoch234
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mckoch234 commented Jul 25, 2024 via email

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7 participants
@wtwt5237 @LiMo-bioxer @xiaocong3333 @martina811 @Pedramto89 @mckoch234 @longyingda