Error Message in SCINA about scina HOT 9 CLOSED

Hello Jon-Xu,

I revisited my SCINA code to check how I solved my problem. I believe that, back in January, I solved this problem by using the SCINA-provided function
markers <- preprocess.signatures('marker_gene_file.csv')
to solve the problem.

I hope this helps!

Best,
Philip

from scina.

Hi,

Thanks for your interest in SCINA! The question you have may result from very different causes. Would you mind sharing a sample count matrix and the signatures that could replicate your bug? You may also send your data to [email protected]. I'll be glad to inspect and figure out the issue for you.

Thanks again for letting me know your problem!

Best regards, Ze

from scina.

Hi Ze,

thanks for the quick reply! I looked into my code again and found a tiny error that resulted in the problem. Having used other classifiers previously, I assumed the use of a binary marker gene matrix was ok. Having gone through the instructions again, I found that I need to use a marker list. With this change, the script is running perfectly. Thank you very much for the great tool, the assignments seem to be very close to what I expected upon visual inspection.

Best regards,
Philip

from scina.

Hi Philip,

Thanks for your update! It's glad to hear that you fixed the problem, and our tool worked very well for you.

Wish you all the best of luck with your work!

Best regards, Ze

from scina.

@jcao89757 I met similar issue, and your email didn't work when I tried to send the data to your for your advice.
Could you please kindly inform your new email address, pls?

from scina.

Hi Jon-xu,
I am one of Ze's friend.
(1) Reason why she did not respond:
Ze has passed away at Oct this year.
We are in a very painful situation.
(2) Possible alternative solution:
If you want to communicate with the related developer, please contact her PhD mentor: Wang, Tao.
https://qbrc.swmed.edu/labs/wanglab/aboutpi.php
(3) Another alternative:
From the feedback we can see that, SCINA is important to this field.
Can we community get together to help maintain this repo?

Best regards,
Wei

from scina.

Thanks Wei and Philip!

from scina.

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.

from scina.

#23

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