Hi,
I tried to use the MFA function and all the time I am getting the same error.
I have the following data.frame:
> az
X patientID years_to_birth vital_status days_to_death
1 TCGA-GM-A2DA TCGA-GM-A2DA 46 1 6593
2 TCGA-GM-A3XG TCGA-GM-A3XG 46 0 0
3 TCGA-GM-A3XN TCGA-GM-A3XN 44 0 0
4 TCGA-HN-A2OB TCGA-HN-A2OB 45 1 1900
5 TCGA-LD-A66U TCGA-LD-A66U 44 0 0
6 TCGA-MS-A51U TCGA-MS-A51U 44 0 0
7 TCGA-OL-A5D8 TCGA-OL-A5D8 40 0 0
8 TCGA-OL-A66I TCGA-OL-A66I 36 0 0
9 TCGA-OL-A66O TCGA-OL-A66O 39 0 0
10 TCGA-PL-A8LZ TCGA-PL-A8LZ 29 0 0
11 TCGA-PL-A8LY TCGA-PL-A8LY 30 0 0
12 TCGA-GM-A2DB TCGA-GM-A2DB 62 0 0
13 TCGA-GM-A2D9 TCGA-GM-A2D9 69 1 1812
14 TCGA-GM-A5PV TCGA-GM-A5PV 63 0 0
15 TCGA-LD-A74U TCGA-LD-A74U 79 0 0
16 TCGA-LL-A5YL TCGA-LL-A5YL 64 0 0
17 TCGA-LL-A6FQ TCGA-LL-A6FQ 77 0 0
18 TCGA-LL-A6FP TCGA-LL-A6FP 90 0 0
19 TCGA-LQ-A4E4 TCGA-LQ-A4E4 73 0 0
20 TCGA-OL-A66K TCGA-OL-A66K 72 1 1275
21 TCGA-S3-AA12 TCGA-S3-AA12 82 0 0
22 TCGA-S3-AA11 TCGA-S3-AA11 67 0 0
days_to_last_followup tumor_tissue_site pathologic_stage pathology_T_stage
1 0 breast stage iib t2
2 1330 breast stage iiia t3
3 2019 breast stage iiia t1c
4 0 breast stage iib t2
5 646 breast stage iib t2
6 681 breast stage iib t2
7 973 breast stage iib t3
8 714 breast stage iia t1c
9 528 breast stage iib t2
10 302 breast stage iiib t4b
11 8 breast stage iib t3
12 2406 breast stage iia t2
13 0 breast stage i t1c
14 412 breast stage iib t2
15 402 breast stage iiic t3
16 519 breast stage iib t2
17 80 breast stage iiia t2
18 677 breast stage iia t2
19 849 breast stage iiia t3
20 0 breast stage iia t2
21 574 breast stage iiia t3
22 421 breast stage iia t2
pathology_N_stage pathology_M_stage gender date_of_initial_pathologic_diagnosis
1 n1b m0 female 1993
2 n1a m0 female 2009
3 n2a m0 female 2007
4 n1 m0 female 0
5 n1mi mx female 2012
6 n1 m0 female 2012
7 n0 mx female 2009
8 n1mi mx female 2008
9 n1a mx female 2012
10 n2 m0 female 2013
11 n0 m0 female 2013
12 n0 (i-) m0 female 2006
13 n0 (i-) m0 female 2006
14 n1a m0 female 2011
15 n3a m0 female 2013
16 n1a mx female 2012
17 n2a mx female 2013
18 nx mx female 2012
19 n1a mx female 2011
20 n0 mx female 2010
21 n1a mx female 2013
22 n0 m0 female 2013
days_to_last_known_alive radiation_therapy histological_type
1 0 yes infiltrating ductal carcinoma
2 0 yes infiltrating lobular carcinoma
3 0 yes infiltrating lobular carcinoma
4 0 yes infiltrating lobular carcinoma
5 0 yes infiltrating lobular carcinoma
6 0 yes infiltrating lobular carcinoma
7 0 yes infiltrating ductal carcinoma
8 0 yes infiltrating ductal carcinoma
9 0 yes infiltrating ductal carcinoma
10 0 no infiltrating ductal carcinoma
11 0 no infiltrating ductal carcinoma
12 0 yes infiltrating ductal carcinoma
13 0 yes infiltrating ductal carcinoma
14 0 no infiltrating lobular carcinoma
15 0 no other, specify
16 0 yes infiltrating lobular carcinoma
17 0 no infiltrating ductal carcinoma
18 0 no infiltrating lobular carcinoma
19 0 yes infiltrating lobular carcinoma
20 0 no infiltrating lobular carcinoma
21 0 no infiltrating ductal carcinoma
22 0 yes infiltrating ductal carcinoma
number_of_lymph_nodes race ethnicity
1 2 white not hispanic or latino
2 3 white not hispanic or latino
3 5 white not hispanic or latino
4 2 0 0
5 2 white not hispanic or latino
6 2 white not hispanic or latino
7 0 black or african american not hispanic or latino
8 0 black or african american not hispanic or latino
9 3 black or african american not hispanic or latino
10 0 black or african american not hispanic or latino
11 0 black or african american not hispanic or latino
12 0 white not hispanic or latino
13 0 white not hispanic or latino
14 1 white not hispanic or latino
15 11 white not hispanic or latino
16 3 white not hispanic or latino
17 7 black or african american not hispanic or latino
18 0 white not hispanic or latino
19 3 white not hispanic or latino
20 0 white not hispanic or latino
21 2 black or african american not hispanic or latino
22 0 black or african american not hispanic or latino
I tried to do this:
res <- MFA(az, group=c(15,16,18),type=c(rep("c",3)),
ncp=5, name.group=c("A","B","C"),num.group.sup=c(1,6))
and everytime I am getting the same error:
Error in MFA(az, group = c(15, 16, 18), type = c(rep("c", 3)), ncp = 5, :
not convenient group definition
Could you please help me with that?
Zsanett