[adegenet-forum] Doubt with DAPC without prior K (find.clusters)

[HELENA IBANEZ MARTINEZ]

  HELENA IBANEZ MARTINEZ <him21024 at um.es> escribió:

> HELENA IBANEZ MARTINEZ <him21024 at um.es> escribió:
>
>> HELLO, MY NAME IS HELENA,
>>
>> I HAVE A QUESTION ABOUT MY DAPC ANALAYSES.
>>
>> I'M FOLLOWING THE TUTORIAL STEP BY STEP AND I GET THE DAPC GRAPH OF MY
>> DATA VERY WELL, BUT MY PROBLEM IS WHEN I REPEAT THE PROCESS MY GRAPHIC
>> RESULTS COME OUT COMPLETELY DIFFERENT EVERY TIME...
>>
>> MY QUESTION IS, WHY DO SUCH DIFFERENT RESULTS COME OUT IF I'M REPEATING
>> EXACTLY THE SAME (SAME DATA AND SAME PARAMETERS)? IT HAPPENS TO ME
>> EVERY TIME I DO IT. WHAT CAN I BE DOING WRONG?
>>
>> HERE I LEAVE THE EXAMPLE OF MY CODE: 135 INDIVIDUALS WITH 8 LOCI
>> SAMPLED IN 6 DIFFERENT LOCATIONS
>>
>> PERCA <-READ.STRUCTURE("PERCAPOPNAME.STR",
>>                                     
ONEROWPERIND=TRUE,
>>                                     
N.IND=135,
>>                                     
N.LOC=8,
>>                                     
COL.LAB=1,
>>                                     
COL.POP=2,
>>                                     
ROW.MARKNAMES=1,
>>                                     
ASK=FALSE)
>>
>> PERCA_GRP6 <-FIND.CLUSTERS(PERCA, MAX.N.CLUST = 10)
>> 200
>> 6
>>
>> DAPC6 <-DAPC(PERCA, PERCA_GRP6$GRP)
>> 200
>> 5
>>
>> SCATTER(DAPC6)
>>
>> THANK YOU.
>>
>> Hi, my name is Helena,
>>
>> I have a question about my DAPC analayses.
>>
>> I'm following the tutorial step by step and well, I get the DAPC graph
>> of my data, but the problem is that when I repeat this my graphic
>> results come out completely different, therefore they are not
>> reliable...
>> My question is, why do such different results come out if I'm repeating
>> exactly the same? It happens to me every time I do it. What can I be
>> doing wrong?
>>
>> Here my code:
>>
>> perca <-read.structure("PercaPopName.str",
>>
                                     
onerowperind=TRUE,
>>
                                     
n.ind=135,
>>
                                     
n.loc=8,
>>
                                     
col.lab=1,
>>
                                     
col.pop=2,
>>
                                     
row.marknames=1,
>>
                                     
ask=FALSE)
>>
>> dapc1 <-dapc(perca, perca_grp$grp)
>>
>> 200
>> 6
>>
>> scatter(dapc1)
>>
>> HELLO AGAIN, I`M HELENA, SORRY BUT I INTRODUCED MY CODE WRONG YESTERDAY:
>>
>> THIS IS MY CODE:
>>
>> PERCA <-READ.STRUCTURE("PERCAPOPNAME.STR",
>>                                     
ONEROWPERIND=TRUE,
>>                                     
N.IND=135,
>>                                     
N.LOC=8,
>>                                     
COL.LAB=1,
>>                                     
COL.POP=2,
>>                                     
ROW.MARKNAMES=1,
>>                                     
ASK=FALSE)
>>
>> PERCA_GRP6 <-FIND.CLUSTERS(PERCA, MAX.N.CLUST = 10)
>> 200
>> 6
>>
>> DAPC6 <-DAPC(PERCA, PERCA_GRP6$GRP)
>> 200
>> 5
>>
>> SCATTER(DAPC6)
>>
>> THANK YOU
>>  
>
>  
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