getting error while using osmFISH Mouse SS Cortex tutorial

[shakesber89]

Hi Guys
Good day. I was recently using the updated osm Fish mouse tutorial. I have installed the latest Giooto 4 . when i try to run the code i have the follwing error. I have used your old code without any problem.

Describe the Error

on

Kindly assist

Jesu

[jiajic]

Hi @shakesber89,
Thank you for reporting this. That tutorial is using some accessors and flex functions that have recently become internals. We will update it shortly.

Best,
George

[shakesber89]

Thanks George.

[jiajic]

Hi @shakesber89,

This tutorial has been updated, and should be working now. It does require a reinstall of Giotto first to patch a bug in one of the functions used.

Best,
George

[shakesber89]

Thanks George. Really appreciated. Best, Jesu

…

On Sun, Feb 4, 2024 at 8:18 PM George Chen ***@***.***> wrote: Hi @shakesber89 <https://github.com/shakesber89>, This tutorial has been updated, and should be working now. It does require a reinstall of *Giotto* first to patch a bug in one of the functions used. Best, George — Reply to this email directly, view it on GitHub <#875 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE3YL3Z373MJBNW73IAQBFLYSAXQBAVCNFSM6AAAAABCMOHBYWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRWGA2DSNZRGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Jesuchristopher Joseph PhD Research Associate Senior Department of Surgery Duke University Durham North Carolina ***@***.***

[shakesber89]

Hi George
Can you share the url link where the code has been updated. I cant able to find the update code in both the old and the current Gioot 4.0 page.

Best,
Jesu

[jiajic]

Of course: https://drieslab.github.io/Giotto/articles/osmfish_mouse_ss_cortex.html

edit: http://giottosuite.com/ should be redirecting to https://drieslab.github.io/Giotto/ I hope.

[shakesber89]

Hi George
Thanks for sharing the url. I was trying the tutorial and go the follwing error when trying PCA.

Kindly assist.
Best,
Jesu

[shakesber89]

I am using Matrix 1.6-2.

[jiajic]

Yes, this is a known issue with the newer Matrix version and how it interacts with irlba (which BiocSingular is using for this computation). Try reinstalling both from source and see if that fixes it.

install.packages("Matrix", type = "source")
install.packages("irlba", type = "source")

This fix is from this thread and you can find more details about this issue within: bwlewis/irlba#70 (comment)

[shakesber89]

Awesome. It worked.

Thanks for your quick response. Really Appreciated.

Best,
Jesu

[jiajic]

Closing as completed. Feel free to reopen if there are any other issues with this vignette.