User: blacktomato27

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Posts by blacktomato27

<prev • 25 results • page 1 of 3 • next >
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how to make groups or strucuration of individuals in R?
... Hi to all Good Morning I have 93 individuals with 395 SNPs genotype data with me and there is no population information available for those individuals. Now I would like group those individuals into certain groups based on their genetic similarity but not like dendrogram. I checked DAPC function in ...
R written 5 weeks ago by blacktomato2720
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why pvclust is not identifying significant clusters?
... Dear all good evening i am making bootstrap dendrogram in R and goal is to identify siginificant clusters out of tree with PVCLUST package. I am getting only two major clusters and not getting significant subclusters eventhough AU/BP values are greater than 95. can any one help me to find out where ...
R written 6 weeks ago by blacktomato2720
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How to calculate LD values of SNP based on chromosomal positions and their call rate?
... Hi to all Good Afternoon I have file containing SNPs (affy 44k chip) with their call rate and chromosomal positions with me and these belongs to rice crop. Now how can i calculate LD values (r2) for these SNPs, my basic objective is to select tag SNPs based on LD for genotyping work. any help with ...
R snp written 7 weeks ago by blacktomato2720
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Comment: C: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Dear Kevin thanks lot for your help and your code working perfectly Great help Regards ...
written 9 weeks ago by blacktomato2720
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Answer: A: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Dear Kevin Good Morning Thanks lot for your help and time spent on solving my problem. I formatted my data as you suggested like 0,1,2 but for some reason it is not working as expected, ok leave it I will go through PVCLUST package only. I would like to know how I can use your above function to run ...
written 10 weeks ago by blacktomato2720
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how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Hi to all Good Afternoon I would like to make genetic tree with SNP genotyping data contains data of 20 genotypes with 394 markers and the same would like to validate with bootstrapping technique. This is my data https://www.dropbox.com/s/7mimhjh94550uaq/SNP%20genotyping%20data.csv?dl=0 Now I am ...
R written 10 weeks ago by blacktomato2720
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Answer: A: how to compare 1st row and 1st column value with rest of the row values in R?
... Dear Friederike Good Morning Thanks lot for your time in helping to solve my query. I will follow your recommendation to make separate file for ever separate parent pair and it will easy to understand and no confusion. @cristian thanks for your recommendation to this useful course in R Once thanks ...
written 11 weeks ago by blacktomato2720
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Answer: A: how to compare 1st row and 1st column value with rest of the row values in R?
... Dear Friederike Thank you very much for your kind and prompt reply to my request. I just modified your code little bit, till last step it is working fine but finally I am unable to format off_par. Now I am sharing my data file (https://www.dropbox.com/s/tysf6p3xdin9lop/biostars.xlsx?dl=0) and code ...
written 11 weeks ago by blacktomato2720
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Answer: A: how to compare 1st row and 1st column value with rest of the row values in R?
... Dear Both Cristian and Friederike Good Afternoon I have one more small query on your answer, will this code work if i want to repeat this analysis for next set like (different parents and individuals) like this Ind M1 M2 M3 M4 M5 1 P1 A/A Unused G/A T/T T/T 2 P2 T/T A/A A/A A/A G/G ...
written 11 weeks ago by blacktomato2720
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Answer: A: how to compare 1st row and 1st column value with rest of the row values in R?
... Dear Both Cristian and Friederike Good Morning Thanks lot for your help and time spent to solve my problem. Both of your code working perfectly and I am getting results as per my wish Once again thanks Regards, ...
written 12 weeks ago by blacktomato2720

Latest awards to blacktomato27

Scholar 10 weeks ago, created an answer that has been accepted. For A: how to compare 1st row and 1st column value with rest of the row values in R?
Popular Question 17 months ago, created a question with more than 1,000 views. For Snp Selection For Genotyping
Popular Question 17 months ago, created a question with more than 1,000 views. For Perl Script To Select Snp Assays
Popular Question 3.3 years ago, created a question with more than 1,000 views. For how to make separate scatter graphs for separate groups with same format in R?

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