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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Trying to load data in Seurat 2.x-generated object #2923

Closed amikomae closed 4 years ago

amikomae commented 4 years ago

Trying to load any plot of our data that was generated on Seurat 2.x build on a computer with Seurat 3.1.5. Experiencing issues, never been able to load this data on this computer. Tried installing Seurat 2.3 but unable to. Hoping for guidance. Do I need to update the data format? is it possible? Really hoping to avoid starting completely from scratch with counts matrices. THANKS!

Example of errors:

VlnPlot(data) Error in UseMethod(generic = "DefaultAssay", object = object) : no applicable method for 'DefaultAssay' applied to an object of class "seurat" TSNEPlot(data) Error in UseMethod(generic = "DefaultAssay", object = object) : no applicable method for 'DefaultAssay' applied to an object of class "seurat"

samuel-marsh commented 4 years ago

Hi,

After loading the Seurat object into R run UpdateSeuratObject(data) first and then you should be all set.

Best, Sam

amikomae commented 4 years ago

Thanks so much, Sam. I tried your suggestion of UpdateSeuratObject(data) after loading the libraries and the data but unfortunately anytime I tried to plot the data I received an error:

TSNEPlot(data) Error in UseMethod(generic = "DefaultAssay", object = object) : no applicable method for 'DefaultAssay' applied to an object of class "seurat" DimPlot(data) Error in UseMethod(generic = "DefaultAssay", object = object) : no applicable method for 'DefaultAssay' applied to an object of class "seurat"

Do you have any further thoughts on what might be wrong or how to troubleshoot? Thanks so much, A

From: Samuel Marsh notifications@github.com Reply-To: satijalab/seurat reply@reply.github.com Date: Wednesday, April 29, 2020 at 6:02 AM To: satijalab/seurat seurat@noreply.github.com Cc: "Uchida, Amiko M.,M.D." AMUCHIDA@mgh.harvard.edu, Author author@noreply.github.com Subject: Re: [satijalab/seurat] Trying to load data in Seurat 2.x-generated object (#2923)

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Hi,

After loading the Seurat object into R run UpdateSeuratObject(data) first and then you should be all set.

Best, Sam

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mojaveazure commented 4 years ago

Your object is a v2 object, not a v3 object. When you ran UpdateSeuratObject, you didn't save the object, so it didn't get updated. Please see https://github.com/satijalab/seurat/issues/990#issuecomment-444606845 for more details about v2 vs v3 objects.