Closed diegoalexespi closed 3 years ago
Hi,
Thank you for this detailed error report. Before going into the problem, could you try the current version of sctransform in the develop
branch?
remotes::install_github("ChristophH/sctransform@develop")
Installing from the current version in the develop
branch appears to have worked, thank you so much! There are no more errors of this kind apparent. This seems related to issue #65 in case that helps others.
Hi, I'm getting the same error. I’ve installed the current version of sctransform from the develop branch, but it seems not work for me Here's my commands and error messages
>sob<-CreateSeuratObject(
countMetrix,
project = projectid,
assay = "RNA",
names.field = 1,
names.delim = "_",
meta.data = NULL,
min.cells = 5,
min.features = 500
)
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
>sob_sct <- SCTransform(sob,verbose=TRUE)
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 17032 by 428
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 428 cells
| | 0%Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In trigamma(th + y) : NaNs produced
2: In trigamma(th) : NaNs produced
Any advice would be appreciated!
The maximum number of features (i.e. genes) detected in the matrix you provided is 198. When I create the Seurat object with min.features = 500
it removes all cells from the downstream analysis and fails. When I set the limit to 5 all cells pass and sctransform works.
The full matrix from your example looks bigger, but I don't know exactly what is causing the error. If you have updated sctransform and Seurat, make sure to restart your R session.
Thanks a lot! I restart R session then it works.
Hi. I am receiving the following error on my counts data when attempting to use the
vst
function.The error only appears when using either
method = "nb_fast"
ormethod = "poisson"
withtheta_estimation_fun = "theta.ml"
. The error disappears when usingmethod = "glmGamPoi"
ormethod = "qpoisson"
. The error also disappears formethod = "nb_fast"
andmethod = "poisson"
if I usetheta_estimation_fun = "theta.mm"
. Moreover, the error appearance for"nb_fast"
and"poisson"
depends on the seed:It seems that the error also ends at similar places for
nb_fast
andpoisson
when the seed is the same for both:Any help is appreciated! Happy to provide more information to help as best as I can. I tried to reproduce the error with
pbmc_small
andpbmc3k
, but I have not been able to. Here is mysessionInfo()
: