FrederickHuangLin ANCOMBC issues

FrederickHuangLin / ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

https://www.nature.com/articles/s41467-020-17041-7

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issues

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Contrast matrices for trend test not square

#296 microbemarsh opened 6 days ago
0
structural zeros interpretation

#295 simone-anza opened 1 week ago
0
Possible bug in `.iter_remle` function

#294 colinvwood opened 1 week ago
0
Improbably huge log-fold change values

#293 LLansing opened 3 weeks ago
0
Regularization of covariance matrix by winsorizing the eigenvalues

#292 FarnazFouladi opened 3 weeks ago
0
NULL results for global, pairwise and pattern analysis

#291 otaviolovison opened 1 month ago
0
Issue with SECOM functions; Updates to DescTools::Winsorize

#290 bpark67 closed 1 month ago
1
Issue with unclassified taxa Inflating DA analysis at specified taxonomic levels in ANCOM-BC2

#289 aimirza opened 1 month ago
0
Different result from ancombc 2.0 and ancombc 2.6

#288 BangzhuoTongUU opened 2 months ago
2
Correct passing of arguments to Winsorize.

#287 zclaas closed 1 month ago
0
Quick question: is pseudo_sens cutoff based on adjusted p-value?

#286 aimirza opened 2 months ago
0
bug fix for ancombc2 when a similar function with model.matrix function is loaded from AlgDesign package

#285 ChiLiubio closed 1 month ago
0
Question about small sample size

#284 UniAlberta opened 2 months ago
2
R crashes when running random effects on longitudinal data

#283 maggiemmurphy opened 2 months ago
0
Error in { : task 1 failed - "missing value where TRUE/FALSE needed"

#282 TsvetkovN closed 1 month ago
1
Setting fix_formula with variables

#281 UniAlberta opened 2 months ago
1
Warning: longer object length is not a multiple of shorter object length

#280 xpolak37 closed 2 months ago
1
Different taxonomy level aggregration and extracting full taxonomic classification.

#279 microb123 opened 3 months ago
0
Beginner encountering error with secom_linear() : Error in DescTools::Winsorize(x, probs = wins_quant, na.rm = TRUE) : unused arguments (probs = wins_quant, na.rm = TRUE)

#278 millermorganOSU closed 1 month ago
1
Question regarding taxon-specific biases

#277 jorondo1 opened 3 months ago
0
Dunnett test is more stringent than pairwise test

#276 LLansing opened 4 months ago
1
ancom model equation

#275 DennisBeest opened 4 months ago
1
Add data sanity check

#274 Maggie8888 closed 2 months ago
0
q-values (adjusted p-values) too low for continuous variable

#272 Pantalius opened 5 months ago
0
Error for specific dataset when using rand_formula "contrasts can be applied only to factors with 2 or more levels"

#271 tybonic opened 5 months ago
1
Testing interactions: global test using F test with approximate degrees of freedom instead of LRT

#270 giulianonetto opened 5 months ago
1
object 'passed_ss_age' not found

#269 JiaLonghao1997 opened 5 months ago
1
added fix for case where nu0, beta have different lengths

#268 pbradz closed 2 months ago
0
NAs and 1s in ancombc2 primary result table

#266 lmartinezgili opened 6 months ago
4
Interpreting error when running ancombc2 function: Error in is.infinite(o1) : default method not implemented for type 'list'

#265 411an13 opened 6 months ago
1
"Error: subscript contains invalid names" when running ancombc2

#264 tfccheng closed 1 month ago
3
Feature Request: Support for Using Taxa as Explanatory Variables in ANCOMBC2

#263 aimirza opened 7 months ago
0
global test and pairwise comparisons giving pvals of all NA or all 1

#262 jpkarl opened 7 months ago
1
Failure to install ANCOMBC neither windows nor Ubuntu

#261 emankhalaf closed 1 month ago
1
Extract normalised counts for linear models outside of ANCOMBC?

#260 charlesfoster opened 7 months ago
0
Help with ancombc2 analysis with repeated measures

#259 tillenglert opened 7 months ago
0
Error in { : task 1 failed - "values must be length 1, but FUN(X[[2]]) result is length 0"

#257 EL9856 opened 7 months ago
1
Pseudo-count sensitivity testing when no pseudo-counts are added

#256 vmaffei opened 7 months ago
0
Visualization the output of ancombc2

#254 J5886 opened 8 months ago
1
Different results with ancombc2 depending on the order of the taxa

#253 laetitia-schramm opened 9 months ago
1
Continuous variable as main variable of interest

#252 ChloePZS closed 1 month ago
2
Installing ANCOMBC

#251 AritriSanyal closed 9 months ago
2
Interpreting negative lfc values for "intercept" in primary result

#250 vmglynn closed 1 month ago
2
R session aborted while running ANCOMBC2

#249 dana-binyamin closed 1 month ago
2
passed_ss_ not found

#248 cmetadea opened 9 months ago
4
ANCOM_BC2's Global test approach?

#247 aimirza opened 9 months ago
1
Additive log-ratio on counts vs proportions

#246 aimirza opened 9 months ago
0
Models used for DA and binomial outcomes

#245 aimirza opened 9 months ago
1
ancombc2 output fmt length exceeds maximal format length 8192

#243 Hesham999666 opened 10 months ago
2
Error in `[.data.frame`(ss_flag, fix_eff) : undefined columns selected

#242 Kris-Abdul closed 1 month ago
1