Open ZhengYingqi-doctor opened 7 months ago
Hi @ZhengYingqi-doctor thanks for your question. The "X" input argument for fit_topic_model()
and de_analysis
should be the same, otherwise you will get errors such as the one you got here.
The "X" for fit_topic_model() is "counts":
> dim(counts)
[1] 15726 27197
But after running fit <- fit_topic_model(counts,k = 16)
, the number of genes was changed:
> dim(fit$F);dim(fit$L)
[1] 24141 16
[1] 15726 16
@ZhengYingqi-doctor Did you get a warning that looked something like this? "One or more columns of X are all zero; after removing all-zero columns, n columns will be used for model fitting."
When I run de_analysis(), there was an error:
The "counts" is a dgCMatrix
And I found that the "fit" only has 24141 genes after run
> fit <- fit_topic_model(t(counts),k = n.topics)
. So how to solve this issue