LDA

Input

Two datasets, one for training and one for testing LDA

Example training dataset:

id	S01	S02	S03	S04	S05	S06	S07	S08	S09	S10	S11	S12	S13	S14	S15	S16	S17	S18	S19	S20	S21	S22	S23	S24	S25	S26	S27	S28	S29	S30	S31	S32	S33	S34	S35	S36	S37	S38
class	Type_L	Type_L	Type_L	Type_L	Type_CL	Type_L	Type_L	Type_L	Type_L	Type_B	Type_CL	Type_L	Type_L	Type_B	Type_B	Type_B	Type_B	Type_L	Type_B	Type_B	Type_B	Type_L	Type_N	Type_N	Type_N	Type_L	Type_L	Type_L	Type_CL	Type_L	Type_L	Type_B	Type_L	Type_CL	Type_B	Type_L	Type_B	Type_L
ENSG00000000419	5.32	5.3	6.64	5.6	6.61	5.24	6.66	6.62	6.41	5.19	6.16	7.29	4.78	6.14	5.66	5.8	6.2	4.69	6.5	5.49	7.29	5.23	5.63	4.82	5.64	6.07	4.79	6.25	5.19	5.8	4.63	5.98	6.19	4.97	4.15	5.82	6.4	4.67
ENSG00000001036	6.11	4.8	4.47	4.99	6.94	5	5.11	5.42	4.58	4.74	6.03	5.47	4.32	6.16	5.89	5.37	6.01	4.72	5.17	5.96	6.35	5.02	5.31	6.37	5.24	6.29	5.81	4.16	6.56	5.91	5.19	4	5.48	4.14	5.9	5.51	5.14	6.22
ENSG00000001084	5.78	4.01	5.14	5.11	3.63	5.93	4.11	3.68	3.23	5.01	5.81	4.5	5.17	5.61	6.19	5.02	6.79	5.97	4.77	5.85	4.78	4.27	6.8	6.25	4.5	5.08	5.21	4.24	4.12	6	4.16	3.19	4.29	3.95	5.26	6.63	4.38	6.38
…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…

Example testing dataset:

id	T01	T02	T03	T04	T05	T06	T07	T08	T09	T10	T11	T12	T13	T14
ENSG00000000419	6.06	5.25	5.15	5.36	5.22	5.75	4.79	6.01	6.39	7.71	5.7	5.85	5.34	5.07
ENSG00000001036	4.47	5.39	5.28	5.82	5.75	6.96	6.09	5.07	5.3	5.76	5.4	4.27	5.03	5.68
ENSG00000001084	4.47	6	5.77	5.76	5.76	4.64	4.07	4.52	4.16	3.24	4.35	2.49	5.89	4.37
ENSG00000001497	5.27	4.27	6.58	5.54	5.57	6.4	4.91	4.79	4.95	5.83	4.89	5.33	4.23	6.03
…	…	…	…	…	…	…	…	…	…	…	…	…	…	…

Code

R Code to run LDA

Output

LDA_prediction_train

Sample	TrueClass	PredictedClass
S01	Type_L	Type_L
S02	Type_L	Type_L
S03	Type_L	Type_L
S04	Type_L	Type_L
S05	Type_CL	Type_CL
S06	Type_L	Type_L
S07	Type_L	Type_L
S08	Type_L	Type_B
S09	Type_L	Type_L
S10	Type_B	Type_B
S11	Type_CL	Type_CL
S12	Type_L	Type_L
S13	Type_L	Type_L
S14	Type_B	Type_B
S15	Type_B	Type_B
S16	Type_B	Type_B
S17	Type_B	Type_L
S18	Type_L	Type_L
S19	Type_B	Type_B
S20	Type_B	Type_B
S21	Type_B	Type_B
S22	Type_L	Type_L
S23	Type_N	Type_B
S24	Type_N	Type_N
S25	Type_N	Type_N
S26	Type_L	Type_L
S27	Type_L	Type_L
S28	Type_L	Type_L
S29	Type_CL	Type_B
S30	Type_L	Type_L
S31	Type_L	Type_L
S32	Type_B	Type_B
S33	Type_L	Type_L
S34	Type_CL	Type_CL
S35	Type_B	Type_B
S36	Type_L	Type_L
S37	Type_B	Type_N
S38	Type_L	Type_L

LDA_prediction_test

Sample	Class
T01	Type_B
T02	Type_B
T03	Type_B
T04	Type_B
T05	Type_B
T06	Type_CL
T07	Type_B
T08	Type_L
T09	Type_L
T10	Type_L
T11	Type_L
T12	Type_L
T13	Type_L
T14	Type_L

Predict_stat

Overall accuracy for the training set: 0.8684211 Confusion matrix:

True predicted	Type_B	Type_CL	Type_L	Type_N
Type_B	9	1	1	1
Type_CL	0	3	0	0
Type_L	1	0	19	0
Type_N	1	0	0	2

LDA plot