Entering edit mode
Hello everyone! To gain familiarity with enrichment analysis, I'm using a model organism to understand how the packages work. Then, I'll be able to conduct analyses on my non-model organism, which presents various challenges, and for which I've opened another question.
Here the code, thank you!
> #read
de <- read.table('de.txt')
de
V1
1 PA1148
2 PA2300
3 PA3408
4 PA2386
5 PA2377
6 PA0852
7 PA2397
8 PA4739
9 PA2427
10 PA4175
11 PA3406
12 PA2127
13 PA5482
14 PA3049
15 PA2069
16 PA3724
17 PA3924
18 PA3479
19 PA0707
20 PA2366
21 PA3519
22 PA1168
23 PA2384
24 PA2393
25 PA2939
26 PA2392
27 PA1245
28 PA1934
29 PA4222
30 PA2398
31 PA3923
32 PA0572
33 PA1249
34 PA3839
35 PA3405
36 PA2165
37 PA1169
38 PA2068
39 PA3337
40 PA4306
41 PA2761
42 PA0122
43 PA4141
44 PA2365
45 PA3570
46 PA2162
47 PA1874
48 PA0818
49 PA2160
50 PA3518
51 PA3018
52 PA4142
53 PA3478
54 PA4648
55 PA2413
56 PA4218
57 PA3574a
58 PA5481
59 PA2114
60 PA3784
61 PA1137
62 PA4348
63 PA3404
64 PA5058
65 PA4139
66 PA4231
67 PA1546
68 PA4467
69 PA2403
70 PA3407
71 PA1871
72 PA3860
73 PA3785
74 PA2385
75 PA2396
76 PA3369
77 PA5440
78 PA4181
79 PA3922
80 PA2184
81 PA0996
82 PA2747
83 PA3791
84 PA4918
85 PA2367
86 PA0997
87 PA1877
88 PA0527
89 PA2161
90 PA1869
91 PA0999
92 PA3930
93 PA2394
94 PA4364
95 PA4223
96 PA1673
97 PA3523
98 PA4224
99 PA2395
100 PA2369
101 PA3786
102 PA2411
103 PA1000
104 PA2753
105 PA2412
106 PA4143
107 PA3522
108 PA2425
109 PA5208
110 PA0252
111 PA0792
112 PA2151
113 PA2592
114 PA3913
115 PA2152
116 PA3600
117 PA4296
118 PA3361
119 PA2153
120 PA2312a
121 PA2478
122 PA2570
123 PA1001
124 PA2399
125 PA2553
126 PA2476
127 PA4621
128 PA2371
129 PA3613
130 PA2424
131 PA0049
132 PA4328
133 PA0050
134 PA4610
135 PA2164
136 PA4229
137 PA5150
138 PA4468
139 PA2116
140 PA3920
141 PA4140
142 PA2144
143 PA4197
144 PA2588
145 PA2390
146 PA4365
147 PA1130
148 PA1196
149 PA1914
150 PA4228
151 PA4225
152 PA1429
153 PA2163
154 PA0051
155 PA3370
156 PA4542
157 PA3601
158 PA3929
159 PA4577
160 SPA0117
161 PA2180
162 PA2404
163 PA3569
164 PA1248
165 PA1875
166 PA5219
167 PA1076
168 PA0024
>
> #as.character
dec <- as.character(de)
dec
[1] "c(\"PA1148\", \"PA2300\", \"PA3408\", \"PA2386\", \"PA2377\", \"PA0852\", \"PA2397\", \"PA4739\", \"PA2427\", \"PA4175\", \"PA3406\", \"PA2127\", \"PA5482\", \"PA3049\", \"PA2069\", \"PA3724\", \"PA3924\", \"PA3479\", \"PA0707\", \"PA2366\", \"PA3519\", \"PA1168\", \"PA2384\", \"PA2393\", \"PA2939\", \"PA2392\", \"PA1245\", \"PA1934\", \"PA4222\", \"PA2398\", \"PA3923\", \"PA0572\", \"PA1249\", \"PA3839\", \"PA3405\", \"PA2165\", \"PA1169\", \"PA2068\", \"PA3337\", \"PA4306\", \"PA2761\", \"PA0122\", \"PA4141\", \"PA2365\", \"PA3570\", \"PA2162\", \"PA1874\", \"PA0818\", \"PA2160\", \"PA3518\", \n\"PA3018\", \"PA4142\", \"PA3478\", \"PA4648\", \"PA2413\", \"PA4218\", \"PA3574a\", \"PA5481\", \"PA2114\", \"PA3784\", \"PA1137\", \"PA4348\", \"PA3404\", \"PA5058\", \"PA4139\", \"PA4231\", \"PA1546\", \"PA4467\", \"PA2403\", \"PA3407\", \"PA1871\", \"PA3860\", \"PA3785\", \"PA2385\", \"PA2396\", \"PA3369\", \"PA5440\", \"PA4181\", \"PA3922\", \"PA2184\", \"PA0996\", \"PA2747\", \"PA3791\", \"PA4918\", \"PA2367\", \"PA0997\", \"PA1877\", \"PA0527\", \"PA2161\", \"PA1869\", \"PA0999\", \"PA3930\", \"PA2394\", \"PA4364\", \"PA4223\", \"PA1673\", \"PA3523\", \"PA4224\", \"PA2395\", \"PA2369\", \n\"PA3786\", \"PA2411\", \"PA1000\", \"PA2753\", \"PA2412\", \"PA4143\", \"PA3522\", \"PA2425\", \"PA5208\", \"PA0252\", \"PA0792\", \"PA2151\", \"PA2592\", \"PA3913\", \"PA2152\", \"PA3600\", \"PA4296\", \"PA3361\", \"PA2153\", \"PA2312a\", \"PA2478\", \"PA2570\", \"PA1001\", \"PA2399\", \"PA2553\", \"PA2476\", \"PA4621\", \"PA2371\", \"PA3613\", \"PA2424\", \"PA0049\", \"PA4328\", \"PA0050\", \"PA4610\", \"PA2164\", \"PA4229\", \"PA5150\", \"PA4468\", \"PA2116\", \"PA3920\", \"PA4140\", \"PA2144\", \"PA4197\", \"PA2588\", \"PA2390\", \"PA4365\", \"PA1130\", \"PA1196\", \"PA1914\", \"PA4228\", \n\"PA4225\", \"PA1429\", \"PA2163\", \"PA0051\", \"PA3370\", \"PA4542\", \"PA3601\", \"PA3929\", \"PA4577\", \"SPA0117\", \"PA2180\", \"PA2404\", \"PA3569\", \"PA1248\", \"PA1875\", \"PA5219\", \"PA1076\", \"PA0024\")"
>
> #no symbols
> decs <- gsub("[\"\n]", "", dec)
> decs
[1] "c(PA1148, PA2300, PA3408, PA2386, PA2377, PA0852, PA2397, PA4739, PA2427, PA4175, PA3406, PA2127, PA5482, PA3049, PA2069, PA3724, PA3924, PA3479, PA0707, PA2366, PA3519, PA1168, PA2384, PA2393, PA2939, PA2392, PA1245, PA1934, PA4222, PA2398, PA3923, PA0572, PA1249, PA3839, PA3405, PA2165, PA1169, PA2068, PA3337, PA4306, PA2761, PA0122, PA4141, PA2365, PA3570, PA2162, PA1874, PA0818, PA2160, PA3518, PA3018, PA4142, PA3478, PA4648, PA2413, PA4218, PA3574a, PA5481, PA2114, PA3784, PA1137, PA4348, PA3404, PA5058, PA4139, PA4231, PA1546, PA4467, PA2403, PA3407, PA1871, PA3860, PA3785, PA2385, PA2396, PA3369, PA5440, PA4181, PA3922, PA2184, PA0996, PA2747, PA3791, PA4918, PA2367, PA0997, PA1877, PA0527, PA2161, PA1869, PA0999, PA3930, PA2394, PA4364, PA4223, PA1673, PA3523, PA4224, PA2395, PA2369, PA3786, PA2411, PA1000, PA2753, PA2412, PA4143, PA3522, PA2425, PA5208, PA0252, PA0792, PA2151, PA2592, PA3913, PA2152, PA3600, PA4296, PA3361, PA2153, PA2312a, PA2478, PA2570, PA1001, PA2399, PA2553, PA2476, PA4621, PA2371, PA3613, PA2424, PA0049, PA4328, PA0050, PA4610, PA2164, PA4229, PA5150, PA4468, PA2116, PA3920, PA4140, PA2144, PA4197, PA2588, PA2390, PA4365, PA1130, PA1196, PA1914, PA4228, PA4225, PA1429, PA2163, PA0051, PA3370, PA4542, PA3601, PA3929, PA4577, SPA0117, PA2180, PA2404, PA3569, PA1248, PA1875, PA5219, PA1076, PA0024)"
> #KEGG analysis
kk <- enrichKEGG(decs, organism="pae", pvalueCutoff=0.05, pAdjustMethod="BH", qvalueCutoff=0.1)
--> No gene can be mapped....
--> Expected input gene ID: PA3896,PA2323,PA3112,PA5453,PA2023,PA1609
--> return NULL...
James showed you in his post below what format
decsshould be in order to have it compatible withenrichKEGG, so that question is 'formally' answered.Based on your previous posts on the support forum it is clear you are struggling with performing GO or KEGG-based enrichment analysis on your list of identifiers. Yet, the only thing I/we know is that these ids are somehow related to the bug Acinetobacter baumannii, but what ids exactly your are working with is still unclear to me. So, I strongly encourage you to be more clear on what exactly you try to achieve! You would do this by describing what type of experiment you actually did (sequencing, proteomics, ...), how your processed the output, including which method and reference genome or proteome you used for that, and by showing a summary/list of (say) 15 real identifiers your are working with.