My dataset have 6000 spcies and i use Tune_ConQuR remove batch effect,the error shows:
result_tuned = Tune_ConQuR(tax_tab=species, batchid=batchid, covariates=group,
batch_ref_pool=c("1","2"),
logistic_lasso_pool=T,
quantile_type_pool=c("standard", "lasso"),
simple_match_pool=T,
lambda_quantile_pool=c(NA, "2p/n"),
interplt_pool=F,
frequencyL=0,
frequencyU=1,num_core = 8)
'adonis' will be deprecated: use 'adonis2' instead
Error in { :
task 15 failed - "contrasts can be applied only to factors with 2 or more levels"
In addition: There were 50 or more warnings (use warnings() to see the first 50)
warnings()
警告信息:
1: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
2: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
3: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
4: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
5: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
6: glm.fit: fitted probabilities numerically 0 or 1 occurred
7: glm.fit: fitted probabilities numerically 0 or 1 occurred
8: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
9: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
10: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
11: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
12: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
13: In lognet(xd, is.sparse, ix, jx, y, weights, offset, alpha, ... :
one multinomial or binomial class has fewer than 8 observations; dangerous ground
14: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
15: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
16: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
17: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
18: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
19: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
20: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
21: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
22: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
23: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
24: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
25: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
26: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
27: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
28: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
29: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
30: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
31: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
32: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
33: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
34: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
35: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
36: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
37: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
38: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
39: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
40: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
41: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
42: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
43: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
44: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
45: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
46: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
47: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
48: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
49: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
50: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique
My dataset have 6000 spcies and i use Tune_ConQuR remove batch effect,the error shows: result_tuned = Tune_ConQuR(tax_tab=species, batchid=batchid, covariates=group,