jasonxu0109 / plantphonedb Goto Github PK

Hi,
I encountered a problem while using PlantPhoneDB:

Error in t.test.default(random, mu = tmp.LR$Score[x], alternative = "less") :
data are essentially constant
Calls: LRscore -> lapply -> FUN -> t.test -> t.test.default

Can you provide me with some advice?

Dear PlantPhoneDB team,

Thanks for developing this tool! I am trying to apply this in my dataset which has about 80k cells. Then it failed with error.
I tried to reduce the size by subsetting out only one dataset, however it again giving me error. I will be grateful if you could help me overcome this issue.

Rahul

1st error with big integrated data

score_data <- LRscore(ra.integrated@assays$SCT@data, LRdb=LR_pair, cluster = Idents(ra.integrated), min.pct = 0.1,iterations=100, method='Average')
Error in asMethod(object) :
Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102

2nd error with only 808 cells

dim(ra.integrated_jb)
[1] 26987 808

score_data <- LRscore(ra.integrated_jb@assays$SCT@data, LRdb=LR_pair, cluster = Idents(ra.integrated_jb), min.pct = 0.1,iterations=100, method='Average')
Error in apply(tmp, 1, function(x) { : dim(X) must have a positive length