I am attempting to use the omu_anova function in the omu package for a set of metabolomics data. My code is the following,
metab_anova <- omu_anova(count_data = metab9, metadata = metabmeta4,
response_variable = "Metabolite",
var1 = "tertiles", var2 = "Race",
interaction = TRUE, log_transform = TRUE, p_adjust = "BH")
where metab9 is my metabolite count table with 17 columns labeled as: Metabolite, KEGG, and then 15 sample columns. metabmeta4 is my metadata dataframe with 4 columns, one of which is labeled Sample and has 15 values matching the 15 column names from the count table.
When I run the function I get this warning and error:
Warning in data.frame(..., check.names = FALSE) : row names were found from a short variable and have been discarded Error in data.frame(lapply(data_Transpose[, nums], function(x) as.numeric(as.integer(x))), : row names supplied are of the wrong length
Ive double checked that the columns from the count data and values from the metadata Sample column match and used the duplicated() function to see if there were any repeats. Results from dput(metab9$Metabolite) are
dput(metab9$Metabolite)
c("10-HYDROXYDECANOATE [M-H]", "1-AMINOCYCLOPROPANECARBOXYLATE [M-H]",
"1-METHYL-L-HISTIDINE [M+H]", "1-METHYL-L-HISTIDINE [M+Na]",
"1-METHYL-L-HISTIDINE [M-H]", "2',4'-DIHYDROXYACETOPHENONE [M+H]",
"2-AMINOISOBUTYRATE [M+H]", "2-AMINOISOBUTYRATE [M-H]", "2-DEOXY-D-GLUCOSE [M-H]",
"2-HYDROXY-4-(METHYLTHIO)BUTANOATE [M-H]", "2-HYDROXYBUTYRATE [M-H]",
"2-HYDROXYBUTYRATE [M-H2O-H]", "2-HYDROXYPHENYLACETATE [M+H]",
"2-HYDROXYPHENYLACETATE [M-H]", "2-METHYLBUTANAL [M+NH4+]", "2-OXOADIPATE [M-H]",
"3-(2-HYDROXYPHENYL)PROPANOATE [M-H]", "3,4-DIHYDROXYPHENYLGLYCOL [M-H2O-H]",
"3-HYDROXYBUTANOATE [M-H]", "3-HYDROXYMETHYLGLUTARATE [M-H]",
"3-METHOXY-4-HYDROXYMANDELATE [M-H]", "4-ACETAMIDOBUTANOATE [M+H]",
"4-HYDROXY-3-METHOXYPHENYLGLYCOL [M-H2O-H]", "4-HYDROXYBENZOATE [M-H]",
"4-PYRIDOXATE [M-H]", "5-AMINOLEVULINATE [M-H]", "ACETOIN [M-H]",
"ALPHA-D-GLUCOSE [M-H2O-H]", "ALPHA-HYDROXYISOBUTYRATE [M-H]",
"ALPHA-HYDROXYISOBUTYRATE [M-H2O-H]", "ALPHA-TOCOPHEROL [M-H]",
"AMINOADIPATE [M+H]", "AMINOADIPATE [M-H]", "AMINOISOBUTANOATE [M+H]",
"ANSERINE [M+H]", "ARABITOL [M-H]", "ARACHIDATE [M-H]", "ASPARAGINE [M+2Na-H]",
"ASPARAGINE [M+H]", "ASPARAGINE [M+Na]", "ASPARAGINE [M+Na-2H]",
"ASPARAGINE [M-H]", "ASPARAGINE [M-H2O-H]", "ASPARTATE [M+H]",
"ASPARTATE [M-H]", "BETAINE [M+H]", "BETAINE [M+Na]", "BETAINE [M-H]",
"Bile Acid_b-Muricholic Acid [M-H]", "Bile Acid_b-Muricholic Acid [M-H+Acetate]",
"Bile Acid_Cholic Acid [M-H+Acetate]", "Bile Acid_Glycochenodeoxycholic Acid [M-H]",
"Bile Acid_Glycodeoxycholic Acid [M-H]", "Bile Acid_Glycoursodeoxycholic Acid [M-H]",
"Bile Acid_Taurocholic Acid [M-H]", "Bile Acid_Ursodeoxycholic acid [M-H]",
"Bile Acid_Ursodeoxycholic acid [M-H+Acetate]", "BILIRUBIN [M+H]",
"BILIRUBIN [M-H]", "BILIVERDIN [M+H]", "BIOTIN [M+H]", "BIS(2-ETHYLHEXYL)PHTHALATE [M+H]",
"BIS(2-ETHYLHEXYL)PHTHALATE [M+Na]", "CAPRYLATE [M-H]", "CHENODEOXYCHOLATE [M-H]",
"CHOLATE [M+NH4+]", "CHOLATE [M-H]", "CITRATE [M-H]", "CITRULLINE [M+2Na-H]",
"CITRULLINE [M+H]", "CITRULLINE [M+Na]", "CITRULLINE [M+Na-2H]",
"CITRULLINE [M-H]", "CITRULLINE [M-NH3+H]", "CORTISOL [M-H]",
"CREATINE [M+H]", "CREATINE [M+Na]", "CREATINE [M+Na-2H]", "CREATINE [M-H]",
"CREATININE [M+H]", "CREATININE [M+Na]", "CREATININE [M-H]",
"CYTIDINE [M-H]", "CYTOSINE [M+H]", "DECANOATE [M-H]", "DEHYDROASCORBATE [M-H]",
"DEOXYCARNITINE [M+H]", "DIACETYL [M-H]", "DIDECANOYL-GLYCEROPHOSPHOCHOLINE [M+Na]",
"D-MANNOSAMINE [M+H]", "DOCOSAHEXAENOATE [M-H]", "Docosanoid_19,20-EpDPA [M-H]",
"D-ORNITHINE [M+H]", "D-ORNITHINE [M-H]", "D-ORNITHINE [M-H2O+H]",
"EIC_1", "EIC_103", "EIC_105", "EIC_106", "EIC_11", "EIC_111",
"EIC_120", "EIC_122", "EIC_124", "EIC_125", "EIC_128", "EIC_129",
"EIC_13", "EIC_131", "EIC_132", "EIC_133", "EIC_140", "EIC_146",
"EIC_149", "EIC_15", "EIC_161", "EIC_177", "EIC_180", "EIC_189",
"EIC_191", "EIC_2", "EIC_215", "EIC_22", "EIC_220", "EIC_228",
"EIC_23", "EIC_237", "EIC_24", "EIC_25", "EIC_26", "EIC_27",
"EIC_28", "EIC_31", "EIC_33", "EIC_345", "EIC_352", "EIC_46",
"EIC_62", "EIC_7", "EIC_71", "EIC_72", "EIC_73", "EIC_74", "EIC_77",
"EIC_78", "EIC_79", "EIC_80", "EIC_89", "Eicosanoid_11,12-EET [M-H]",
"Eicosanoid_11-HETE [M-H+Acetate]", "Eicosanoid_11t LTD4 [M-H]",
"Eicosanoid_12,13 diHOME [M-H]", "Eicosanoid_12-HETE [M-H+Acetate]",
"Eicosanoid_12-HHTrE [M-H]", "Eicosanoid_12-OPDA [M-H+Acetate]",
"Eicosanoid_12oxo LTB4 [M-H]", "Eicosanoid_12-oxoETE [M-H]",
"Eicosanoid_12S-HpEPE [M-H]", "Eicosanoid_13,14-dihydro-15-keto-PGA2 [M-H]",
"Eicosanoid_13,14-dihydro-PGE1 [M-H]", "Eicosanoid_13-HODE [M-H]",
"Eicosanoid_13-oxoODE [M-H]", "Eicosanoid_13-oxoODE [M-H+Acetate]",
"Eicosanoid_14,15-diHETrE [M-H]", "Eicosanoid_15d PGA2 [M-H]",
"Eicosanoid_15-epi-PGA1 [M-H+Acetate]", "Eicosanoid_15-HETE [M-H]",
"Eicosanoid_15-keto-PGA1 [M-H+Acetate]", "Eicosanoid_15-oxoETE [M-H]",
"Eicosanoid_17(18) EpETE [M-H+Acetate]", "Eicosanoid_19,20 DiHDPA [M-H]",
"Eicosanoid_20cooh AA [M-H]", "Eicosanoid_5(S) HETrE [M-H]",
"Eicosanoid_5(S) HETrE [M-H+Acetate]", "Eicosanoid_5,15-diHETE [M-H]",
"Eicosanoid_5S-HpEPE [M-H]", "Eicosanoid_5S-HpETE [M-H]", "Eicosanoid_6,15 dk-,dh- PGF1a [M-H]",
"Eicosanoid_8(9)-EpETE [M-H]", "Eicosanoid_8(S) HETrE [M-H]",
"Eicosanoid_8,12-iso-iPF2à-VI-1,5-lactone [M-H+Acetate]", "Eicosanoid_8,15-diHETE [M-H+Acetate]",
"Eicosanoid_8-HETE [M-H]", "Eicosanoid_8-iso-PGA1 [M-H]", "Eicosanoid_8-iso-PGA1 [M-H+Acetate]",
"Eicosanoid_9(S) HOTrE [M-H]", "Eicosanoid_9,10 diHOME [M-H]",
"Eicosanoid_Arachidonic Acid [M-H]", "Eicosanoid_DHA [M-H]",
"Eicosanoid_dhk PGF2a [M-H]", "Eicosanoid_EPA [M-H]", "Eicosanoid_HXB3 [M-H]",
"Eicosanoid_HXB3 [M-H+Acetate]", "Eicosanoid_PGK1 [M-H+Acetate]",
"Eicosanoid_tetranor 12(R) HETE [M-H+Acetate]", "ELAIDATE [M-H]",
"Endocannabinoid_2-Arachidonyl glycerol ether [M-H+Acetate]",
"Endocannabinoid_D-erythro-Sphingosine C-18 [M-H+Acetate]", "Endocannabinoid_N-oleoyl Dopamine [M-H]",
"Endocannabinoid_Oleoyl Ethanolamide [M-H+Acetate]", "ERYTHRITOL [M-H]",
"ESTRADIOL-17ALPHA [M-H2O+H]", "ETHYL 3-INDOLEACETATE [M-H]",
"ETHYLMALONATE [M+Na-2H]", "FAHFA_11", "FAHFA_12", "FAHFA_14",
"FAHFA_15", "FAHFA_18", "FAHFA_22", "FAHFA_25", "FAHFA_27", "FAHFA_28",
"FAHFA_3", "FAHFA_37", "FAHFA_39", "FAHFA_57", "FAHFA_58", "FAHFA_62",
"FAHFA_69", "FFA_Adrenic Acid [M-H]", "FFA_Adrenic Acid [M-H+Acetate]",
"FFA_a-linolenic Acid [M-H]", "FFA_a-linolenic Acid [M-H+Acetate]",
"FFA_Arachidic Acid [M-H]", "FFA_Arachidic Acid [M-H+Acetate]",
"FFA_Arachidonic Acid [M-H]", "FFA_Behenic Acid [M-H]", "FFA_Behenic Acid [M-H+Acetate]",
"FFA_Dihomo-g-linolenic [M-H+Acetate]", "FFA_Docosadienoic Acid [M-H]",
"FFA_Docosaenoic Acid [M-H]", "FFA_Docosapentaenoic Acid [M-H]",
"FFA_Docosatrienoic Acid [M-H]", "FFA_Docosatrienoic Acid [M-H+Acetate]",
"FFA_Eicosadienoic Acid [M-H]", "FFA_Eicosadienoic Acid [M-H+Acetate]",
"FFA_Eicosapentaenoic Acid [M-H]", "FFA_Eicosapentaenoic Acid [M-H+Acetate]",
"FFA_Eicosatrienoic Acid [M-H]", "FFA_Eicosenoic Acid [M-H+Acetate]",
"FFA_Gondolic Acid [M-H]", "FFA_Gondolic Acid [M-H+Acetate]",
"FFA_Heptadecaenoic Acid [M-H]", "FFA_Heptadecaenoic Acid [M-H+Acetate]",
"FFA_Heptadecanoic Acid [M-H]", "FFA_Lignoceric Acid [M-H]",
"FFA_Linoleic Acid [M-H]", "FFA_Myristic Acid [M-H]", "FFA_Myristic Acid [M-H+Acetate]",
"FFA_Nervonic Acid [M-H]", "FFA_Oleic Acid [M-H+Acetate]",
"FFA_Palmitoleic Acid [M-H]", "FFA_Palmitoleic Acid [M-H+Acetate]",
"FFA_Pentadecanoic Acid [M-H]", "FFA_Petroselenic Acid [M-H]",
"FFA_Petroselenic Acid [M-H+Acetate]", "FFA_Stearic Acid [M-H+Acetate]",
"FFA_Stearidonic Acid [M-H]", "FFA_Tricosanoic Acid [M-H]",
"FFA_Tricosenoic Acid [M-H]", "FUMARATE [M-H]", "GALACTURONATE [M-H]",
"GAMMA-AMINOBUTYRATE [M-H]", "GLUCONATE [M+Na-2H]", "GLUCONATE [M-H]",
"GLUTAMATE [M+2Na-H]", "GLUTAMATE [M+H]", "GLUTAMATE [M+Na-2H]",
"GLUTAMATE [M-H]", "GLUTAMATE [M-H2O-H]", "GLUTAMINE (13C5 STABLE ISOTOPE) [M+H]",
"GLUTAMINE (13C5 STABLE ISOTOPE) [M-H]", "GLUTAMINE [M+2Na-H]",
"GLUTAMINE [M+H]", "GLUTAMINE [M+Na]", "GLUTAMINE [M+Na-2H]",
"GLUTAMINE [M-H]", "GLUTAMINE [M-H2O-H]", "GLUTAMINE [M-NH3+H]",
"GLYCEROL [M-H]", "GLYCOCHOLATE [M+H]", "GLYCOCHOLATE [M-H]",
"GLYCOLATE [M-H]", "GUANIDINOACETATE [M+H]", "GUANIDINOACETATE [M-H]",
"GUANINE [M+H]", "GUANOSINE [M+H]", "HEPTADECANOATE [M-H]", "HEPTANOATE [M-H]",
"HIPPURATE [M+H]", "HIPPURATE [M-H]", "HIPPURATE [M-H2O-H]",
"HISTIDINE [M+Na-2H]", "HOMOSERINE [M+H]", "HYDROXYKYNURENINE [M-H]",
"HYDROXYPHENYLLACTATE [M+Na-2H]", "HYDROXYPHENYLLACTATE [M-H]",
"HYPOTAURINE [M+H]", "HYPOTAURINE [M-H]", "HYPOXANTHINE [M+H]",
"HYPOXANTHINE [M+Na]", "HYPOXANTHINE [M+Na-2H]", "HYPOXANTHINE [M-H]",
"INDOLE [M+H]", "INDOLE-3-METHYL ACETATE [M-H]", "INDOLE-3-PYRUVATE [M-H]",
"INOSINE [M+H]", "INOSINE [M+Na]", "INOSINE [M-H]", "Int_Std_12,13-diHOME",
"Int_Std_12-HETE", "Int_Std_13,14-dihydro-15-keto-PGD2", "Int_Std_13,14-dihydro-15-keto-PGF2a",
"Int_Std_13-HODE", "Int_Std_15-deoxy-d12,14-PGJ2", "Int_Std_15-HETE",
"Int_Std_20-HETE", "Int_Std_5-oxoETE", "Int_Std_5S-HETE", "Int_Std_6-keto-PGF1a",
"Int_Std_9,10-diHOME", "Int_Std_9-HODE", "Int_Std_CUDA", "Int_Std_LTB4",
"Int_Std_PGD2", "Int_Std_PGE2", "Int_Std_PGF2a", "Int_Std_Resolvin D1",
"Int_Std_TXB2", "ISOCITRATE [M-H]", "ISOLEUCINE [M+H]", "ISOLEUCINE [M-H]",
"KETOLEUCINE [M-H]", "KYNURENATE [M+H]", "KYNURENINE [M+H]",
"KYNURENINE [M-H]", "LACTATE [M-H]", "LACTATE [M-H2O-H]", "LACTOSE [M+NH4+]",
"L-ALANINE [M-H]", "LAURATE [M-H]", "LAUROYLCARNITINE [M+H]",
"L-CARNITINE [M+H]", "LEUCINE [M+H]", "LEUCINE [M-H]", "L-GULONOLACTONE [M-H]",
"LINOLEATE [M-H]", "LITHOCHOLYLTAURINE [M+Na]", "LYSINE (STABLE ISOTOPE) [M+H]",
"LYSINE (STABLE ISOTOPE) [M-H]", "LYSINE [M-H]", "LYSINE [M-H2O+H]",
"MALATE [M-H]", "MALEATE [M-H]", "MANDELATE [M-H]", "MANNITOL [M-H]",
"MANNOSE [M+Na]", "MANNOSE [M-H]", "METHIONINE [M+H]", "METHIONINE [M-H]",
"METHIONINE [M-NH3+H]", "METHYL ACETOACETATE [M-H]", "METHYL GALACTOSIDE [M-H]",
"MONOETHYLMALONATE [M-H2O-H]", "MYOINOSITOL [M-H]", "N,N,N-TRIMETHYLLYSINE [M+H]",
"N6-(DELTA2-ISOPENTENYL)-ADENINE [M+H]", "N6-(DELTA2-ISOPENTENYL)-ADENINE [M-H]",
"N-ACETYLALANINE [M+H]", "N-ACETYLALANINE [M+Na]", "N-ACETYLASPARAGINE [M+H]",
"N-ACETYLASPARAGINE [M-H2O-H]", "N-ACETYLASPARTATE [M-H]", "N-ACETYLGLUCOSAMINE [M+H]",
"N-ACETYLGLUCOSAMINE [M-H2O+H]", "N-ACETYLGLUTAMATE [M+H]", "N-ACETYLGLUTAMATE [M-H]",
"N-ACETYLGLYCINE [M-H]", "N-ACETYLLEUCINE [M+H]", "N-ACETYLMANNOSAMINE [M+H]",
"N-ACETYLMANNOSAMINE [M-H]", "N-ACETYLMANNOSAMINE [M-H2O+H]",
"N-ACETYLMETHIONINE [M-H]", "N-ACETYLNEURAMINATE [M+H]", "N-ACETYLNEURAMINATE [M+Na]",
"N-ACETYLNEURAMINATE [M-H]", "N-ACETYLNEURAMINATE [M-H2O-H]",
"N-ACETYLPHENYLALANINE [M-H]", "N-ACETYLPUTRESCINE [M+H]", "N-ACETYLSERINE [M-H2O-H]",
"N-ALPHA-ACETYLLYSINE [M+H]", "NERVONATE [M-H]", "N-FORMYL-L-METHIONINE [M-H]",
"NICOTINAMIDE [M+H]", "NONANOATE [M-H]", "Novel EIC_1", "Novel EIC_2",
"Novel EIC_28", "Novel EIC_8", "O-ACETYLCARNITINE [M+H]", "O-ACETYLCARNITINE [M-H2O+H]",
"O-ACETYLSERINE [M-H]", "OMEGA-HYDROXYDODECANOATE [M-H]", "OXALATE [M-H]",
"OXOGLUTARATE [M-H]", "PALMITATE [M-H]", "PALMITOLEATE [M-H]",
"PANTOTHENATE [M+H]", "PANTOTHENATE [M+Na-2H]", "PARAXANTHINE [M+H]",
"PENTANOATE [M-H]", "PHENYLALANINE (STABLE ISOTOPE) [M+H]", "PHENYLALANINE (STABLE ISOTOPE) [M-H]",
"PHENYLALANINE [M+H]", "PHENYLALANINE [M-H]", "PHENYLALANINE [M-NH3+H]",
"PHENYLPYRUVATE [M-H]", "PHOSPHORYLCHOLINE [M+H]", "PIPECOLATE [M+H]",
"PIPECOLATE [M-H]", "Polar Molecule_ARACHIDATE [M-H]", "Polar Molecule_CHENODEOXYCHOLATE [M-H+Acetate]",
"Polar Molecule_CORTEXOLONE [M-H+Acetate]", "Polar Molecule_CORTICOSTERONE [M-H+Acetate]",
"Polar Molecule_CORTISOL [M-H+Acetate]", "Polar Molecule_CORTISONE [M-H+Acetate]",
"Polar Molecule_DEOXYCHOLATE [M-H]", "Polar Molecule_DEOXYCHOLATE [M-H+Acetate]",
"Polar Molecule_ELAIDATE [M-H]", "Polar Molecule_GAMMA-LINOLENATE [M-H]",
"Polar Molecule_GAMMA-LINOLENATE [M-H+Acetate]", "Polar Molecule_LINOLEATE [M-H]",
"Polar Molecule_LINOLEATE [M-H+Acetate]", "Polar Molecule_LUMICHROME [M-H]",
"Polar Molecule_MYRISTATE [M-H]", "Polar Molecule_N-ACETYLNEURAMINATE [M-H]",
"Polar Molecule_N-ACETYLTRYPTOPHAN [M-H]", "Polar Molecule_OLEOYL-GLYCEROL [M-H]",
"Polar Molecule_OLEOYL-GLYCEROL [M-H+Acetate]", "Polar Molecule_PALMITATE [M-H+Acetate]",
"Polar Molecule_PALMITOLEATE [M-H]", "Polar Molecule_PALMITOLEATE [M-H+Acetate]",
"Polar Molecule_STEARATE [M-H]", "Polar Molecule_Tetrahydrocortisol [M-H+Acetate]",
"Polar Molecule_TRICOSANOATE [M-H]", "PROLINE [M+2Na-H]", "PROLINE [M+H]",
"PROLINE [M+Na]", "PROLINE [M-H]", "PROPIONATE [M-H]", "Putative_1a-Methyl-5a-androstan-3a,17b-diol glucuronide",
"Putative_1a-Methyl-5a-androstan-3a-ol-17-one glucuronide", "Putative_1-Hexadecanoyl-sn-glycero-3-phosphoethanolamine",
"Putative_1-Oleoyl-sn-glycero-3-phosphoethanolamine", "Putative_1-Palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine",
"Putative_1-Stearoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine",
"Putative_2a-Methyl-5a-androstan-3a-ol-17-one glucuronide", "Putative_2-Hydroxypalmitic acid",
"Putative_3-Hydroxystanozolol glucuronide", "Putative_4-[5-[[4-[5-[acetyl(hydroxy)amino]pentylamino]-4-oxobutanoyl]-hydroxyamino]pentylamino]-4-oxobutanoic acid",
"Putative_4-Androsten-17b-ol-3-one glucosiduronate", "Putative_5a-Androstan-17b-ol-3-one glucosiduronate",
"Putative_5a-Androstan-3a,17b-diol-17b-glucuronide", "Putative_6-((E)-2-((1R,2S,3R,5S)-3,5-Dihydroxy-2-((Z)-oct-2-enyl)cyclopentyl)vinyl)tetrahydro-2H-pyran-2-one",
"Putative_7a,17a-Dimethyl-5b-androstane-3a,17b-diol glucuronide",
"Putative_7-Keto-3a,12-a-dihydroxycholanic acid", "Putative_Androstan-3-ol-17-one 3-glucuronide",
"Putative_Androsterone glucuronide", "Putative_Beta-HC", "Putative_Bilirubin",
"Putative_Chenodeoxycholic acid 24-acyl-b-D-glucuronide", "Putative_CORTISOL",
"Putative_Decylbenzenesulfonic acid", "Putative_Glycocholic acid",
"Putative_Hydrocortisone 21-hemisuccinate", "Putative_Naringenin-7-O--D-Glucuronide / Naringenin-4'-O-b-D-glucuronide",
"Putative_Natamycin", "Putative_N-oleoyl taurine", "Putative_N-Oleoyl-L-serine",
"Putative_Taurolithocholic acid sulfate", "Putative_Tauroursodeoxycholic acid",
"PYRUVATE [M-H]", "QUINOLINATE [M-H]", "RIBOSE [M-H]", "SALICYLATE [M-H]",
"SERINE [M+2Na-H]", "SERINE [M+H]", "SERINE [M-H]", "SORBITOL [M+Na-2H]",
"SORBITOL [M-H]", "STEARATE [M-H]", "Sterol_11-Deoxycorticosterone [M-H+Acetate]",
"Sterol_11-Deoxycortisol [M-H+Acetate]", "Sterol_11-keto-testosterone [M-H+Acetate]",
"TAGATOSE [M+Na]", "TAGATOSE [M-H]", "TAURINE [M+2Na-H]", "TAURINE [M+H]",
"TAURINE [M+Na]", "TAURINE [M+NH4+]", "TAURINE [M-H]", "THEOBROMINE [M-H]",
"THEOPHYLLINE [M-H]", "THREONINE [M+2Na-H]", "THREONINE [M+H]",
"THREONINE [M-H]", "TRANS-4-HYDROXY-L-PROLINE [M+H]", "TRANS-4-HYDROXY-L-PROLINE [M-H]",
"TRANS-CYCLOHEXANEDIOL [M-H]", "TREHALOSE [M+Na]", "TRICOSANOATE [M-H]",
"TRIGONELLINE [M+H]", "TRYPTOPHAN [M+2Na-H]", "TRYPTOPHAN [M+H]",
"TRYPTOPHAN [M+Na]", "TRYPTOPHAN [M+Na-2H]", "TRYPTOPHAN [M-H]",
"TRYPTOPHAN [M-NH3+H]", "TYROSINE [M+2Na-H]", "TYROSINE [M+H]",
"TYROSINE [M+Na]", "TYROSINE [M-H]", "TYROSINE [M-NH3+H]", "URATE [M-H]",
"UREIDOPROPIONATE [M+H]", "UREIDOPROPIONATE [M+Na-2H]", "UREIDOPROPIONATE [M-H]",
"URIDINE [M+Na-2H]", "URIDINE [M-H]", "VALINE [M+2Na-H]", "VALINE [M+H]",
"VALINE [M-H]", "VLCDCA_1", "VLCDCA_12", "VLCDCA_15", "VLCDCA_17",
"VLCDCA_19", "VLCDCA_2", "VLCDCA_23", "VLCDCA_24", "VLCDCA_26",
"VLCDCA_3", "VLCDCA_32", "VLCDCA_33", "VLCDCA_34", "VLCDCA_35",
"VLCDCA_40", "VLCDCA_41", "VLCDCA_42", "VLCDCA_43", "VLCDCA_44",
"VLCDCA_48", "VLCDCA_6", "VLCDCA_8", "XANTHINE [M-H]", "XANTHOSINE [M-H]"
)
Results from dput(metabmeta4$Sample) are below. There are only 15 rows so I am unsure why it is returning more SampleIDs then I have in my dataframe (see metabmeta4$Sample results below)
> dput(metabmeta4$Sample)
structure(c(2L, 4L, 17L, 19L, 14L, 8L, 3L, 1L, 6L, 18L, 12L,
16L, 15L, 9L, 21L), .Label = c("164", "167", "174", "175", "190",
"194", "195", "205", "206", "214", "220", "231", "233", "242",
"246", "257", "259", "260", "267", "314", "323", "343", "344",
"350", "360", "365", "324", "336", "378", "346", "352", "379",
"381", "391", "399", "402", "404", "408", "410", "412", "415",
"417", "418", "419", "421", "423", "427"), class = "factor")
> metabmeta4$Sample
[1] 167 175 259 267 242 205 174 164 194 260 231 257 246 206 323
47 Levels: 164 167 174 175 190 194 195 205 206 214 220 231 233 ... 427
Any suggestions would be helpful!
Here is my hypothesis: Your error results from one or more of the 15 sample columns in the count table (not Metabolite or KEGG) being incorrectly rendered as something other than "numeric" variables.
Looking at the source code for omu_anova, the "Metabolite" column is first assigned to the rownames of the data frame and then the following line selects only the columns in the count data that are numeric.
data_Int <- count_data[sapply(count_data, function(x) is.numeric(x))]
So, here non-numeric columns are dropped, and having too few columns could explain the error you see because the 'Metabolite' rownames are lost when the transposed count data are later joined to the metadata.
To diagnose this try str(metab9) and eyeball whether or not all the sample columns are numeric. Alternatively, check that your 'KEGG' column is not numeric (it should be a factor or character, I suspect). If KEGG is numeric, it would give the count data too many columns.