error in CalcPolyAResiduals function with human PBMC data

[Renown-TAL]

I try the "PASTA vignette", and get a error as fowllowing:

######################## code

pbmc <- CalcPolyAResiduals(pbmc, assay = "polyA", features = features.last.exon, gene.names = "Gene_Symbol", verbose = TRUE)

######################## info

Calculating background distribution
Using all cells in order to estimate background distribution
Removing 321 sites without a gene annotation
Running Dirichlet Multionmial Regression
Regularizing Dirichlet Multionmial Variance
Error in validObject(object = value) :
invalid class "polyAsiteAssay" object: features in 'scale.data' must be in the same order as in 'data'
In addition: Warning messages:
1: The slot argument of AverageExpression() is deprecated as of Seurat 5.0.0.
ℹ Please use the layer argument instead.
ℹ The deprecated feature was likely used in the Seurat package.
Please report the issue at https://github.com/satijalab/seurat/issues.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.
2: In asMethod(object) :
sparse->dense coercion: allocating vector of size 3.1 GiB
3: In .M2v(x) : sparse->dense coercion: allocating vector of size 3.1 GiB
4: In asMethod(object) :
sparse->dense coercion: allocating vector of size 3.1 GiB
5: In asMethod(object) :
sparse->dense coercion: allocating vector of size 3.1 GiB

#######################################

Could you tell me it is the error of Seurat 5.0.0 or PASTA? Thanks in advanced!

[ntsopoul]

I have encountered the same problem. @Renown-TAL were you able to resolve it?

[Renown-TAL]

I have encountered the same problem. @Renown-TAL were you able to resolve it?

I can't.

[mhkowalski]

Hello,

Thanks for your bug report and sorry for our delayed response. I have updated the package to be compatible with Seurat v5, so please try updating your version and let me know if you are continuing to have problems.