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Using SCT assays #136
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Hi @mckoch234 CC @saketkc I'm guessing these are changes with Seurat V5: #133 I didn't change the codebase as I was hoping others would chip in. We could probably make things V5 compatible. @saketkc or others in the Satija Lab might be able to lend a helping hand as well. Please detail the issues you've having; an email might be necessary. Best, Evan |
I have a seurat object that has a sct assay and a v5 rna assay. Even if I
use the sct assay it gives me the same error, same with using the rna assay.
…On Mon, Jul 8, 2024 at 5:11 PM evanbiederstedt ***@***.***> wrote:
Hi @mckoch234 <https://github.com/mckoch234> CC @saketkc
<https://github.com/saketkc>
I'm guessing these are changes with Seurat V5: #133
<#133>
I didn't change the codebase as I was hoping others would chip in.
We could probably make things V5 compatible. @saketkc
<https://github.com/saketkc> or others in the Satija Lab might be able to
lend a helping hand as well.
Please detail the issues you've having; an email might be necessary.
Best, Evan
—
Reply to this email directly, view it on GitHub
<#136 (comment)>,
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.
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I am able to convert the object to a conos object but this happens when
running p2app4conos()
…On Tue, Jul 9, 2024 at 5:16 PM Mark Koch ***@***.***> wrote:
I have a seurat object that has a sct assay and a v5 rna assay. Even if I
use the sct assay it gives me the same error, same with using the rna assay.
On Mon, Jul 8, 2024 at 5:11 PM evanbiederstedt ***@***.***>
wrote:
> Hi @mckoch234 <https://github.com/mckoch234> CC @saketkc
> <https://github.com/saketkc>
>
> I'm guessing these are changes with Seurat V5: #133
> <#133>
>
> I didn't change the codebase as I was hoping others would chip in.
>
> We could probably make things V5 compatible. @saketkc
> <https://github.com/saketkc> or others in the Satija Lab might be able
> to lend a helping hand as well.
>
> Please detail the issues you've having; an email might be necessary.
>
> Best, Evan
>
> —
> Reply to this email directly, view it on GitHub
> <#136 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A25OLKNPDOUQKL6USHOSZFTZLL6BRAVCNFSM6AAAAABKDYQFEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJVGMZDKMBUGU>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
|
Without having the data you are working with, I cannot really debug this given the information you've provided. Here is the function: Lines 365 to 523 in 91110ba
If you run the sections line-by-line, you might be able to track down the bug. That would be helpful. Otherwise, please email the data to me so I could help out. It's not something seen before. Best, Evan |
The organism is mice
…On Tue, Jul 9, 2024 at 7:13 PM Mark Koch ***@***.***> wrote:
Here is the conos object and session info. Compression did not work
https://drive.google.com/file/d/14gFO7dx0WjztHp-v1G2r4keIVNY7Eieu/view?usp=sharing
On Tue, Jul 9, 2024 at 5:28 PM evanbiederstedt ***@***.***>
wrote:
> @mckoch234 <https://github.com/mckoch234>
>
> Without having the data you are working with, I cannot really debug this
> given the information you've provided.
>
> Here is the function:
>
>
> https://github.com/kharchenkolab/conos/blob/91110bafc058fd29aaabb6ef6d381d220cc4e4b6/R/integrations.R#L365-L523
>
> If you run the sections line-by-line, you might be able to track down the
> bug. That would be helpful. Otherwise, please email the data to me so I
> could help out.
>
> It's not something seen before.
>
> Best, Evan
>
> —
> Reply to this email directly, view it on GitHub
> <#136 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A25OLKLN55RRJYWW56YL4E3ZLRIYDAVCNFSM6AAAAABKDYQFEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYG43DCNRTGE>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
|
My apologies, I reran making the conos object and now ran into an error
with con$embedGraph(method = "UMAP"). The object does not have the
embeddings in it.
…On Tue, Jul 9, 2024 at 7:15 PM Mark Koch ***@***.***> wrote:
The organism is mice
On Tue, Jul 9, 2024 at 7:13 PM Mark Koch ***@***.***> wrote:
> Here is the conos object and session info. Compression did not work
>
>
> https://drive.google.com/file/d/14gFO7dx0WjztHp-v1G2r4keIVNY7Eieu/view?usp=sharing
>
> On Tue, Jul 9, 2024 at 5:28 PM evanbiederstedt ***@***.***>
> wrote:
>
>> @mckoch234 <https://github.com/mckoch234>
>>
>> Without having the data you are working with, I cannot really debug this
>> given the information you've provided.
>>
>> Here is the function:
>>
>>
>> https://github.com/kharchenkolab/conos/blob/91110bafc058fd29aaabb6ef6d381d220cc4e4b6/R/integrations.R#L365-L523
>>
>> If you run the sections line-by-line, you might be able to track down
>> the bug. That would be helpful. Otherwise, please email the data to me so I
>> could help out.
>>
>> It's not something seen before.
>>
>> Best, Evan
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#136 (comment)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A25OLKLN55RRJYWW56YL4E3ZLRIYDAVCNFSM6AAAAABKDYQFEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYG43DCNRTGE>
>> .
>> You are receiving this because you were mentioned.Message ID:
>> ***@***.***>
>>
>
|
I am getting this error. Error in
x[[i, drop = TRUE]]
:! 'counts' not found in this Seurat object
Did you mean "nCount_SCT"?
How do I get it to recognize the counts? The seurat objects I'm working with have multiple assays but even when I change the assay it gives me that error.
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