Error with SCINA command

Pedramto89 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

xiaocong3333 commented 1 year ago

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 commented 1 year ago

longyingda commented 1 year ago

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 commented 1 year ago

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.

LiMo-bioxer commented 1 year ago

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

longyingda commented 1 year ago

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

your signature lists contain many overlapped genes, set the parameter 'rm_overlap=FALSE';

check that the name of your maker gene is correct, if the gene is present in your expression matrix;

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. https://github.com/jcao89757/SCINA/issues/8

LiMo-bioxer commented 1 year ago

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

your signature lists contain many overlapped genes, set the parameter 'rm_overlap=FALSE';

check that the name of your maker gene is correct, if the gene is present in your expression matrix;

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 commented 7 months ago

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 commented 1 month ago

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

wtwt5237 commented 1 month ago

Yes. One list of genes for each cell type

Tao

From: Mark Koch @.> Sent: Wednesday, July 24, 2024 0:35 To: jcao89757/SCINA @.> Cc: Tao Wang @.>; Mention @.> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

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mckoch234 commented 1 month ago

I tried including only cells of one immune type (b cells), and normalizing it the way the tutorial said, still getting the same error.

On Wed, Jul 24, 2024 at 12:53 AM Tao Wang @.***> wrote:

Yes. One list of genes for each cell type

Tao

From: Mark Koch @.> Sent: Wednesday, July 24, 2024 0:35 To: jcao89757/SCINA @.> Cc: Tao Wang @.>; Mention @.> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

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wtwt5237 commented 1 month ago

We need at least two cell types. Could you please try again?

Tao

From: Mark Koch @.> Sent: Wednesday, July 24, 2024 12:43 AM To: jcao89757/SCINA @.> Cc: Tao Wang @.>; Mention @.> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

I tried including only cells of one immune type (b cells), and normalizing it the way the tutorial said, still getting the same error.

On Wed, Jul 24, 2024 at 12:53 AM Tao Wang @.<mailto:@.>> wrote:

Yes. One list of genes for each cell type

Tao

From: Mark Koch @.<mailto:@.>> Sent: Wednesday, July 24, 2024 0:35 To: jcao89757/SCINA @.<mailto:@.>> Cc: Tao Wang @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

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mckoch234 commented 1 month ago

I tried again with b cells, monocytes, and nk cells. I still got the same error.

On Wed, Jul 24, 2024 at 9:39 AM Tao Wang @.***> wrote:

We need at least two cell types. Could you please try again?

Tao

From: Mark Koch @.> Sent: Wednesday, July 24, 2024 12:43 AM To: jcao89757/SCINA @.> Cc: Tao Wang @.>; Mention @.> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

I tried including only cells of one immune type (b cells), and normalizing it the way the tutorial said, still getting the same error.

On Wed, Jul 24, 2024 at 12:53 AM Tao Wang @.<mailto:@.>> wrote:

Yes. One list of genes for each cell type

Tao

From: Mark Koch @.<mailto:@.>> Sent: Wednesday, July 24, 2024 0:35 To: jcao89757/SCINA @.<mailto:@.>> Cc: Tao Wang @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

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mckoch234 commented 1 month ago

I tried using an example pbmc dataset and it worked, even without normalizing it.

On Wed, Jul 24, 2024 at 10:29 PM Mark Koch @.***> wrote:

I tried again with b cells, monocytes, and nk cells. I still got the same error.

On Wed, Jul 24, 2024 at 9:39 AM Tao Wang @.***> wrote:

We need at least two cell types. Could you please try again?

Tao

From: Mark Koch @.> Sent: Wednesday, July 24, 2024 12:43 AM To: jcao89757/SCINA @.> Cc: Tao Wang @.>; Mention @.> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

I tried including only cells of one immune type (b cells), and normalizing it the way the tutorial said, still getting the same error.

On Wed, Jul 24, 2024 at 12:53 AM Tao Wang @.<mailto:@.>> wrote:

Yes. One list of genes for each cell type

Tao

From: Mark Koch @.<mailto:@.>> Sent: Wednesday, July 24, 2024 0:35 To: jcao89757/SCINA @.<mailto:@.>> Cc: Tao Wang @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [jcao89757/SCINA] Error with SCINA command (Issue #23)

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jcao89757 / SCINA

Error with SCINA command #23