SCtransform: Will not return corrected UMI because residual type is not set to 'pearson'

[t1nnenissen]

Hi there,

I am running SCtransform with the v2 regularization. However, I am getting a message that I don't know what means:

Can you help me understand what this means/why it is happening?

[hong-hui-zhao]

hello，guys, i meet the question same as you ,do you deal with it ,and you can tell me how to slove this question ?

[DaliBAmor]

did you find a solution plz ?

[hong-hui-zhao]

no

…

---Original--- From: ***@***.***> Date: Thu, May 4, 2023 01:59 AM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [satijalab/seurat] SCtransform: Will not return corrected UMIbecause residual type is not set to 'pearson' (Discussion #6850) did you find a solution plz ? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[arjanboltjes]

It seems to me this has to do with the argument conserve.memory = TRUE, perhaps in combination with vars.to.regress not set to NULL. I had never used the conserve.memory argument until now, and I got the same error. When I remove it, the error is gone. When I use it, but without regressing out any variable, it's also gone. It's unclear to me why this would pop up.

[chloesavignac]

I have the same issue! any updates?

[yesitsjess]

I've started getting the same since adding return.only.var.genes=F to my SCTransform call

[MWRR]

same here. Is there anyone figure it out?