search

hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
Other
170 stars 64 forks source link

Fail to run scde.error.models using example dataset #77

Closed biowilliam closed 5 years ago

biowilliam commented 5 years ago

I have successfully installed SCDE package in R3.5, however I failed to replicate the results and got an empty o.ifm while running scde.error.models following the scde tutorials. The error message is as following. Could anyone else kindly suggest what is the problem here? Many thanks,. ############################################################ ERROR encountered in building a model for cell MEF_68 - skipping the cell. Error: Error in FUN(X[[i]], ...) : trying to get slot "logLik" from an object of a basic class ("function") with no slots ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells ############################################################

biowilliam commented 5 years ago

Solved following https://github.com/hms-dbmi/scde/issues/40 @Jean, I suggest updating the following scde link with the latest stable package http://hms-dbmi.github.io/scde/package.html

wangxlab commented 4 years ago

Hi,

I get the same problem as @biowilliam. I have installed and tried scde_1.99.1 from homepage, scde_2.12.0, or scde-2.14 from Bioconductor on R-3.6.0 I was running "diffexp.Rmd" codes. But scde.error.models got the same error. Please see below. Could you give any recommendation?

############################################################### o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 1, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)

ERROR encountered in building a model for cell MEF_66 - skipping the cell. Error: Error in FUN(X[[i]], ...) : trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_67 - skipping the cell. Error: Error in FUN(X[[i]], ...) : trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_68 - skipping the cell. Error: Error in FUN(X[[i]], ...) : trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells

wangxlab commented 4 years ago

I tried to download an old version scde_1.2.1 and installed. Now, scde.error.models is working. It is strange that newer version doesn't work. When you have time, please give me your help. Thank you!

Sanghoon