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SCINA error #7

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cjhong opened this issue Nov 5, 2019 · 9 comments
Closed

SCINA error #7

cjhong opened this issue Nov 5, 2019 · 9 comments
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@cjhong
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cjhong commented Nov 5, 2019

I constructed gene markers in CSV file format. Make sure that gene symbols are consistent with the exp matrix. When I called SCINA(), I got the following error!


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


@jcao89757
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Hi cj,

Thanks for raising up your question!

Mostly this error indicates that your signature lists so contain many overlapped genes that, after removing overlaps automatically, one or more signature lists may become NULL lists without any genes. Would you like to set the parameter 'rm_overlap=FALSE' and let me know if your question would be solved?

Thanks again for letting me know!

Best regards, Ze

@jcao89757 jcao89757 self-assigned this Nov 6, 2019
@cjhong
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cjhong commented Dec 17, 2019

Thank you, the problem is resolved!

@ankurnaqib
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Hi. I am still facing the same issue. My data file is too big so I am not sure if that is the issue but here is my code that I am running:-

as.data.frame(data@assays$RNA[,]) -> scina.data
load(system.file('extdata','example_signatures.RData', package = "SCINA"))

signatures

SCINA(
scina.data,
signatures,
max_iter = 100,
convergence_n = 10,
convergence_rate = 0.999,
sensitivity_cutoff = 0.9,
rm_overlap=FALSE,
allow_unknown=TRUE,
log_file = 'Scina.log'
) -> scina.results

and the error I am getting is

Error in chol.default(theta[[i]]$sigma1) : 'a' must have dims > 0
In addition: Warning messages:
1: In min(c(diag(x$sigma1), diag(x$sigma2))) :
no non-missing arguments to min; returning Inf
2: In min(c(diag(x$sigma1), diag(x$sigma2))) :
no non-missing arguments to min; returning Inf
3: In min(c(diag(x$sigma1), diag(x$sigma2))) :
no non-missing arguments to min; returning Inf

Any advise would be really helpful. Thanks.

@cjhong
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cjhong commented Jan 24, 2022

As jcao89757 suggested, make sure whether your marker genes for a cell type are a subset of the other.

@simonmfr
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I keep getting the same error without a large gene overlap. It might have to do with fotmatting of the gene names? If i randomly remove some entries from the gene list, it works for me.

@Ivy-ops
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Ivy-ops commented Feb 15, 2022

@cjhong May I know how to make sure "whether your marker genes for a cell type are a subset of the other", if my signatures list is very large? Thanks.

@cjhong
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cjhong commented Feb 16, 2022 via email

@Pedramto89
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Although I put the 'rm_overlap=FALSE', I still get the error. I am sure no overlapping genes are in my signature gene list.

@longyingda
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Although I put the 'rm_overlap=FALSE', I still get the error. I am sure no overlapping genes are in my signature gene list.

#23

1, you need to check that the name of your maker gene is correct;
2, you need to check if the gene is present in your expression matrix;

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