Error: Max dimension too large: objects 1, 2 contain fewer than 30 cells. Please specify a maximum dimensions that is less than the number of cells in any object (3).

KirstLab / asc_seurat

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Error: Max dimension too large: objects 1, 2 contain fewer than 30 cells. Please specify a maximum dimensions that is less than the number of cells in any object (3). #18

Closed DoreenLug closed 2 years ago

DoreenLug commented 2 years ago

Hi I am trying to load multple datasets to asc-seurat but I am unable to form the integration object due to the following error.

Max dimension too large: objects 1, 2 contain fewer than 30 cells. Please specify a maximum dimensions that is less than the number of cells in any object (3).

I will appreciate any assistance : My parameters are

DoreenLug commented 2 years ago

Any help please ?

wendelljpereira commented 2 years ago

Hi @DoreenLug,

Without accessing your dataset would be challenging to understand what is happening.

This message was returned by Seurat package. Following what is described in this issue: https://github.com/satijalab/seurat/issues/3166, it appears that this error is generated when one or more of the samples you are trying to integrate have too few cells. Would that be your case?

For further investigation, I would need to have access to the data, so I could replicate the problem. Would it be something you will be comfortable providing?

You could also try to integrate the samples using Seurat directly, as a way to pinpoint the issue. Here are the instructions for the integration: https://satijalab.org/seurat/articles/integration_introduction.html.

Let me know if this information helps.

Cheers, Wendell

DoreenLug commented 2 years ago

Hi , Okay, I will try the integration directly on Seurat and try to find the issue. Where can I access the number of cells available i n my sample and how can I fit it to asc-seurat?

wendelljpereira commented 2 years ago

Hi @DoreenLug,

This is not a bug of the app, so it is not a high priority. It is related with your sample and/or Seurat's integration pipeline. I recommend you to try running the integration using the command lines of Seurat's tutorial and see what is happening.

I will give it a look when I have time, so please be patient.

Regards, Wendell

wendelljpereira commented 2 years ago

Hi @DoreenLug,

I am sorry, but I did not have the time to try to execute the analysis using your dataset.

I don't see evidence that it is a bug since we have tested the integration using different datasets with no problem.

I am closing this issue if you have no further questions.

Best Regards, Wendell