Installing ALDEx2

ALDEx2 is a bioconductor package that could be installed Via bioconductor

library(BiocManager)
#BiocManager::install('ALDEx2')

ALDEx2 tutorials

Main tutorial

Click

ALDEx2 uses non-parametric statistical modeling

Click

Useful book

Statistical Analysis of Microbiome Data with R

Working with ALDEx2

Dataset dietswap

• Phyloseq dataset From microbiome package dietswap

library(microbiome)
data("dietswap")
dietswap

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 130 taxa by 3 taxonomic ranks ]

• check the number of genera 130

• check the number of samples 222

• The two groups of interest in our Aldex2 analysis are:

• AAM, it means African American

• AFR, it means African

• The whole variables of dietswap dataset are: StCode, StVisit, InterventionGroup, MGDMOGTT1OR2Fi, MGDM1Fi, MGDM2FiNEW, MPrSerumMMP8, MPrSerumphIGFBP1, MPrSerumIGFBP1, MCRP, MPrVagMMP8, MAge1, MprepBMI, MBMIOverwOrObese, MLivingStatus, MUniEdu, MEdu, MPA, MMETINDX, MprepSmoke, MSmoke, MEthnicity, MEkJ, MEkcal, MProg, MHHg, MFatg, MFiballg, ProEPercent, MHHEPercent, MFatEPercent, Mparity, MPRW, MPrAbVag, MPrAbVag4weeks, MPrVaginaTreatment, MPrVaginaTreatmentTotalNo, MPrVaginaTreatment4weeks, MPRAb, MPRAbNo, MPRAb4weeks, MPrevProb1, MPrevProb1withintwoweeks, MPrevProb1beforetwoweeks, MProbUse, MBleedElevBBorAnemia1, allGroups, group

Main tests

t-test

T-test between groups where wi.eBH<= 0.05 and we.eBH <= 0.05. The first tens only.

	wi.eBH	we.eBH
Allistipes et rel.	0.0000000	0.0000000
Anaerostipes caccae et rel.	0.0004071	0.0021022
Bacteroides fragilis et rel.	0.0000252	0.0000110
Bacteroides intestinalis et rel.	0.0000009	0.0000026
Bacteroides ovatus et rel.	0.0000000	0.0000000
Bacteroides plebeius et rel.	0.0000000	0.0000000
Bacteroides splachnicus et rel.	0.0001776	0.0059688
Bacteroides stercoris et rel.	0.0000004	0.0000482
Bacteroides uniformis et rel.	0.0000031	0.0000006
Bacteroides vulgatus et rel.	0.0000000	0.0000000

Kruskal-Wallis test

Kruskal-Wallis test between groups where kw.eBH <=0.05. The first tens only.

	kw.eBH	kw.ep
Allistipes et rel.	0.0000000	0.00e+00
Anaerostipes caccae et rel.	0.0004071	7.16e-05
Bacteroides fragilis et rel.	0.0000252	3.00e-06
Bacteroides intestinalis et rel.	0.0000009	1.00e-07
Bacteroides ovatus et rel.	0.0000000	0.00e+00
Bacteroides plebeius et rel.	0.0000000	0.00e+00
Bacteroides splachnicus et rel.	0.0001776	2.93e-05
Bacteroides stercoris et rel.	0.0000004	0.00e+00
Bacteroides uniformis et rel.	0.0000031	3.00e-07
Bacteroides vulgatus et rel.	0.0000000	0.00e+00

Estimate Effect Size

Estimate Effect Size between groups where the effect > 0.1 or the effect < -0.1, the first tens only.

	rab.all	rab.win.AAM	rab.win.AFR	diff.btw	diff.win	effect	overlap
Akkermansia	2.4333721	2.3264607	2.5920414	0.2718289	2.331340	0.1003826	0.4468000
Alcaligenes faecalis et rel.	-1.2698393	-1.3608975	-1.1478797	0.2714610	2.366439	0.1012274	0.4502000
Allistipes et rel.	3.8782135	3.1801389	5.1119393	1.6625243	2.404121	0.6552559	0.2383523
Anaerostipes caccae et rel.	2.3541216	1.8667819	2.8020553	0.7463802	1.829484	0.3672804	0.3371326
Anaerotruncus colihominis et rel.	2.1989229	2.4109583	1.9022760	-0.2617569	2.225332	-0.1136506	0.4465107
Anaerovorax odorimutans et rel.	0.7969434	0.9100502	0.6716430	-0.2617360	1.194559	-0.2045655	0.4057189
Bacteroides fragilis et rel.	3.6851499	2.7277086	4.4171758	1.1424114	2.570196	0.4303816	0.3289342
Bacteroides intestinalis et rel.	-0.6130119	-1.2377048	0.3646694	1.6472656	3.126962	0.5076885	0.2738000
Bacteroides ovatus et rel.	2.8630332	2.0412264	3.9044801	1.5391897	2.213514	0.6573121	0.2384000
Bacteroides plebeius et rel.	1.9390361	1.2653126	2.5952103	1.2614453	1.784423	0.6575322	0.2352000

Summary

The first 15 only.

	diff.btw	diff.win	effect	overlap	we.ep	wi.ep	we.eBH	wi.eBH
Allistipes et rel.	1.6625243	2.404121	0.6552559	0.2383523	0.0000000	0.0000000	0.0000000	0.0000000
Anaerostipes caccae et rel.	0.7463802	1.829484	0.3672804	0.3371326	0.0004109	0.0000716	0.0021022	0.0004071
Anaerovorax odorimutans et rel.	-0.2617360	1.194559	-0.2045655	0.4057189	0.0272605	0.0473909	0.0620924	0.1014251
Bacteroides fragilis et rel.	1.1424114	2.570196	0.4303816	0.3289342	0.0000012	0.0000030	0.0000110	0.0000252
Bacteroides intestinalis et rel.	1.6472656	3.126962	0.5076885	0.2738000	0.0000003	0.0000001	0.0000026	0.0000009
Bacteroides ovatus et rel.	1.5391897	2.213514	0.6573121	0.2384000	0.0000000	0.0000000	0.0000000	0.0000000
Bacteroides plebeius et rel.	1.2614453	1.784423	0.6575322	0.2352000	0.0000000	0.0000000	0.0000000	0.0000000
Bacteroides splachnicus et rel.	0.5558292	1.407581	0.3456709	0.3274000	0.0013684	0.0000293	0.0059688	0.0001776
Bacteroides stercoris et rel.	1.0565405	1.807949	0.5030065	0.2749450	0.0000068	0.0000000	0.0000482	0.0000004
Bacteroides uniformis et rel.	1.8479531	3.673068	0.4947658	0.2981404	0.0000000	0.0000003	0.0000006	0.0000031
Bacteroides vulgatus et rel.	2.3028431	3.278722	0.6886983	0.2447511	0.0000000	0.0000000	0.0000000	0.0000000
Bifidobacterium	0.5896979	1.978390	0.2738965	0.3558000	0.0041537	0.0005298	0.0154198	0.0025087
Bryantella formatexigens et rel.	0.3458719	1.650042	0.2012445	0.4017197	0.0139609	0.0108863	0.0428020	0.0355833
Bulleidia moorei et rel.	-0.6576048	1.708306	-0.3391389	0.3370000	0.0002358	0.0007945	0.0009883	0.0028710
Catenibacterium mitsuokai et rel.	-1.4408704	3.525224	-0.3484797	0.3212000	0.0003128	0.0000697	0.0014030	0.0003602

ALDEx2 Wrapper

The first 15 only.

	rab.all	rab.win.AAM	rab.win.AFR	diff.btw	diff.win	effect	overlap	we.ep	we.eBH	wi.ep	wi.eBH
Actinomycetaceae	-5.4097921	-5.416925	-5.4025698	0.0460888	4.220298	0.0087526	0.4957009	0.5372296	0.6557136	0.5316953	0.6508055
Aeromonas	-5.6117266	-5.636775	-5.5801023	0.0404607	4.290807	0.0083972	0.4955009	0.4886397	0.6195258	0.4908196	0.6220262
Akkermansia	1.6706992	1.544770	1.8222962	0.2904666	2.412044	0.1083721	0.4428000	0.1877045	0.3525808	0.1542397	0.3072821
Alcaligenes faecalis et rel.	-2.0095630	-2.130209	-1.8519295	0.3554576	2.492967	0.1294209	0.4370000	0.1444239	0.2619220	0.2165351	0.3476054
Allistipes et rel.	3.1790350	2.469320	4.4031057	1.6721978	2.517624	0.6421007	0.2456000	0.0000000	0.0000000	0.0000000	0.0000000
Anaerobiospirillum	-5.5786364	-5.598406	-5.5582017	0.1019949	4.195919	0.0215416	0.4884000	0.5111306	0.6354885	0.4950349	0.6224329
Anaerofustis	-5.5107962	-5.633154	-5.3493605	0.2908242	4.219219	0.0568741	0.4698000	0.4442366	0.5705238	0.4198762	0.5558390
Anaerostipes caccae et rel.	1.5842199	1.172157	2.0647986	0.7505529	1.754072	0.3929324	0.3264000	0.0001496	0.0008357	0.0000346	0.0002257
Anaerotruncus colihominis et rel.	1.4724702	1.643813	1.2286622	-0.2234073	2.213632	-0.0906825	0.4548000	0.4076705	0.5825280	0.2644596	0.4406690
Anaerovorax odorimutans et rel.	0.0534992	0.173551	-0.0880767	-0.2507698	1.207598	-0.1923404	0.4093181	0.0360819	0.0767754	0.0490105	0.1021640
Aquabacterium	-5.2878133	-5.192724	-5.3970588	-0.2566430	4.303852	-0.0516166	0.4707059	0.4371709	0.5713546	0.4429046	0.5751277
Atopobium	-5.2638824	-5.201397	-5.3499520	-0.1134649	4.132625	-0.0238986	0.4860000	0.4897667	0.6157344	0.4960600	0.6210132
Bacillus	-3.2284247	-3.248051	-3.2063139	0.0257078	2.119265	0.0112742	0.4945011	0.5640247	0.6868960	0.5521835	0.6758519
Bacteroides fragilis et rel.	2.9086180	1.986017	3.6797470	1.1709792	2.635873	0.4268490	0.3242000	0.0000029	0.0000270	0.0000070	0.0000605
Bacteroides intestinalis et rel.	-1.3242737	-1.964276	-0.3196531	1.6777492	3.196426	0.5060486	0.2837433	0.0000017	0.0000120	0.0000002	0.0000020

Plots

Bland-Altman plot

• Red taxa are the significant ones with adjusted p-values cutoff 0.05 or less.

• Grey taxa are the rare ones

Median plots

Plot median between-group difference Versus median within-group difference

Effect and Volcano plots